Pals Tax Law Addu 2017 Final-1-1 PDF

Recent
Jurisprudence (April 2014 April 2017) Taxation

A compilation continued by the Philippine Association of Law
Schools (PALS) & Ateneo de Davao for the 2017 Bar Operations

GENERAL PRINCIPLES OF TAXATION

R.A. 9504 (TAX EXEMPTION OF MINIMUM WAGE EARNERS AND INCREASING
PERSONAL/ADDITIONAL EXEMPTIONS / CHANGE IN Optional Standard Deduction) must be
liberally construed. We are mindful of the strict construction rule when it comes to the interpretation
of tax exemption laws. The canon, however, is tempered by several exceptions, one of which is when
the taxpayer falls within the purview of the exemption by clear legislative intent. In this situation, the
rule of liberal interpretation applies in favor of the grantee and against the government. In this case,
there is a clear legislative intent to exempt the minimum wage received by an MWE who earns
additional income on top of the minimum wage. As previously discussed, this intent can be seen from
both the law and the deliberations. Accordingly, we see no reason why we should not liberally
interpret R.A. 9504 in favor of the taxpayers. (JAIME N. SORIANO VS. SECRETARY OF FINANCE AND
THE COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 184450, JANUARY 24, 2017, C.J.
SERENO)

It must be borne in mind that tax exemptions, which respondents obviously want or desire to avail
of in this case, are strictissimi juris. Indeed, taxation is the rule and tax exemption the exception. Tax
exemptions should be granted only by clear and unequivocal provision of law on the basis of language
too plain to be misunderstood, We hold that in this case respondents have utterly failed to make out
even a prima facie for tax exemption in their favor. (BUREAU OF INTERNAL REVENUE VS. MANILA
HOME TEXTILE, INC., GR 203057, JUNE 6, 2016, J. DEL CASTILLO)

In matters of taxation, the government cannot be estopped by the mistakes, errors or omissions of
its agents for upon it depends the ability of the government to serve the people for whose benefit
taxes are collected. (COMMISSIONER OF INTERNAL REVENUE VS. NIPPON EXPRESS (PHILS.)
CORPORATION, G.R. NO. 212920, SEPTEMBER 16, 2015)

It is settled that tax exemptions must be clear and unequivocal. A taxpayer claiming a tax exemption
must point to a specific provision of law conferring on the taxpayer, in clear and plain terms,
exemption from a common burden. Any doubt whether a tax exemption exists is resolved against the
taxpayer. MERALCO has failed to present herein any express grant of exemption from real property
tax of its transformers, electric posts, transmission lines, insulators, and electric meters that is valid
and binding even under the Local Government Code. (MANILA ELECTRIC COMPANY VS. THE CITY
ASSESSOR AND CITY TREASURER OF LUCENA CITY G.R. NO. 166102, AUGUST 5, 2015)

San Roque, held that BIR Ruling No. DA-489-03 was a general interpretative rule because it was a
response to a query made, not by a particular taxpayer, but by a government agency tasked with
processing tax refunds and credits. Thus, it applies to all taxpayers alike, and not only to one
particular taxpayer. (COMMISSIONER OF INTERNAL REVENUE VS. AIR LIQUIDE PHILIPPINES,
INC., G.R. NO. 210646, JULY 29, 2015)

The claim of a taxpayer under a tax amnesty shall be allowed when the liability involves the deficiency
in payment of income tax. However, it must be disallowed when the taxpayer is assessed on his
capacity as a withholding tax agent because the person who earned the taxable income was another
person other than the withholding agent. (LG ELECTRONICS PHILIPPINES, INC. VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 165451, DECEMBER 03, 2014, J. LEONEN)
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Recent Jurisprudence (April 2014 April 2017) Taxation

The Court has consolidated these 3 petitions as they involve the same parties, similar facts and
common questions of law. This is not the first time that Fort Bonifacio Development Corporation
(FBDC) has come to this Court about these issues against the very same respondents (CIR), and the
Court En Banc has resolved them in two separate, recent cases that are applicable here. It is of course
axiomatic that a rule or regulation must bear upon, and be consistent with, the provisions of the
enabling statute if such rule or regulation is to be valid. In case of conflict between a statute and an
administrative order, the former must prevail. To be valid, an administrative rule or regulation must
conform, not contradict, the provisions of the enabling law. An implementing rule or regulation
cannot modify, expand, or subtract from the law it is intended to implement. Any rule that is not
consistent with the statute itself is null and void. To recapitulate, RR 7-95, insofar as it restricts the
definition of "goods" as basis of transitional input tax credit under Section 105 is a nullity. (FORT
BONIFACIO DEVELOPMENT CORPORATION VS. COMMISSIONER OF INTERNAL REVENUE AND
REVENUE DISTRICT OFFICER, REVENUE DISTRICT NO. 44, TAGUIG AND PATEROS, BUREAU OF
INTERNAL REVENUE, G.R. NO. 175707, NOVEMBER 19, 2014, J. LEONARDO-DE CASTRO)

For Double taxation to take place, the two taxes must be imposed on the same subject matter, for the
same purpose, by the same taxing authority, within the same jurisdiction, during the same taxing
period; and the taxes must be of the same kind or character. Because Section 21 of the Revenue Code
of Manila imposed the tax on a person who sold goods and services in the course of trade or business
based on a certain percentage of his gross sales or receipts in the preceding calendar year, while
Section 15 and Section 17 likewise imposed the tax on a person who sold goods and services in the
course of trade or business but only identified such person with particularity, namely, the wholesaler,
distributor or dealer (Section 15), and the retailer (Section 17), all the taxes being imposed on the
privilege of doing business in the City of Manila in order to make the taxpayers contribute to the citys
revenues were imposed on the same subject matter and for the same purpose. (NURSERY CARE
CORPORATION; SHOEMART, INC.; STAR APPLIANCE CENTER, INC.; H&B, INC.; SUPPLIES
STATION, INC.; and HARDWARE WORKSHOP, INC. vs. ANTHONY ACEVEDO, in his CAPACITY AS
THE TREASURER OF MANILA; AND THE CITY OF MANILA, G.R. NO. 180651, JULY 30, 2014, J.
BERSAMIN)

"Time and again, the Court has held that it is a necessary judicial practice that when a court has laid
down a principle of law as applicable to a certain facts, it will adhere to that principle and apply it to
all future cases in which the facts are substantially the same. Stare decisis et non quieta movere, stand
by the decisions and disturb not what is settled. Stare decisis simply means that for the sake of
certainty, a conclusion reached in one case should be applied to those that follow if the facts are
substantially the same, even though the parties may be different. It proceeds from the first principle
of justice that, absent any powerful countervailing considerations, like cases ought to be decided
alike. Thus, where the same questions relating to the same event have been put forward by the parties
similarly situated as in a previous case litigated and decided by a competent court, the rule of stare
decisis is a bar to any attempt to relitigate the same issue." The Court has pronounced in Republic of
the Philippines v. Sunlife Assurance Company of Canada " that under the Tax Code although
respondent is a cooperative, registration with the CDA is not necessary in order for it to be exempt
from the payment of both percentage taxes on insurance premiums, under Section 121; and
documentary stamp taxes on policies of insurance or annuities it grants, under Section 199." The CTA
observed that the factual circumstances obtaining in Sunlife and the present case are substantially
the same. Hence, the CTA based its assailed decision on the doctrine enunciated by the Court in the
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said case. (COMMISSIONER OF INTERNAL REVENUE VS. THE INSULAR LIFE ASSURANCE CO.
LTD., G.R. NO. 197192, JUNE 4, 2014, J. REYES)

An opportunity must be given the internal revenue branch of the government to investigate and
confirm the veracity of the claims of the taxpayer. The absolute freedom that petitioner seeks to
automatically credit tax payments against tax liabilities for a succeeding taxable year, can easily give
rise to confusion and abuse, depriving the government of authority and control over the manner by
which the taxpayers credit and offset their tax liabilities, not to mention the resultant loss of revenue
to the government under such a scheme. (COCA-COLA BOTTLERS PHILIPPINES, INC., vs. CITY OF
MANILA; LIBERTY M. TOLEDO, in her capacity as Officer-in-Charge (OIC), Treasurer of the CITY
OF MANILA; JOSEPH SANTIAGO, IN HIS CAPACITY AS OIC, CHIEF LICENSE DIVISION OF THE
CITY OF MANILA; REYNALDO MONTALBO, IN HIS CAPACITY AS CITY AUDITOR OF THE CITY OF
MANILA, G.R. NO. 197561, APRIL 7, 2014, J. PERALTA)

Since the main purpose of Ordinance No. 18 is to regulate certain construction activities of the
identified special projects, which includes cell sites or telecommunications towers, the fees
imposed in Ordinance No. 18 are primarily regulatory in nature, and not primarily revenue-raising.
While the fees may contribute to the revenues of the Municipality, this effect is merely incidental.
Thus, the fees imposed in Ordinance No. 18 are not taxes. (SMART COMMUNICATIONS INC., vs.
MUNICIPALITY OF MALVAR, BATANGAS, G.R. No. 204429, FEBRUARY 18, 2014, J. CARPIO)

INCOME TAXATION

Thus, this Court held in the above-cited PAL consolidated cases: However, upon the amendment of
the 1997 NIRC, Section 22 of R.A. 9337 abolished the franchise tax and subjected PAL and similar
entities to corporate income tax and value-added tax (VAT). PAL nevertheless remains exempt from
taxes, duties, royalties, registrations, licenses, and other fees and charges, provided it pays corporate
income tax as granted in its franchise agreement. Accordingly, PAL is left with no other option but to
pay its basic corporate income tax, the payment of which shall be in lieu of all other taxes, except VAT,
and subject to certain conditions provided in its charter. It bears to note that the repealing clause of
RA 9337 enumerated the laws or provisions of laws which it repeals. However, there is nothing in
the repealing clause, nor in any other provisions of the said law, which makes specific mention of PD
1590 as one of the acts intended to be repealed. (COMMISSIONER OF INTERNAL REVENUE AND
COMMISSIONER OF CUSTOMS VS. PHILIPPINE AIRLINES, INC., G.R. NO. 215705-07 FEBRUARY
22, 2017, J. PERALTA)

A careful review of the pleadings reveals that there is no countervailing consideration for the Court
to revisit its aforequoted ruling in G.R. Nos. 195909 and 195960 (Commissioner of Internal Revenue
v. St. Luke's Medical Center, Inc.). Thus, under the doctrine of stare decisis, which states that "[o]nce
a case has been decided in one way, any other case involving exactly the same point at issue x x x
should be decided in the same manner," the Court finds that SLMC is subject to l0% income tax insofar
as its revenues from paying patients are concerned. To be clear, for an institution to be completely
exempt from income tax, Section 30(E) and (G) of the 1997 NIRC requires said institution to operate
exclusively for charitable or social welfare purpose. But in case an exempt institution under Section
30(E) or (G) of the said Code earns income from its for-profit activities, it will not lose its tax
exemption. However, its income from for-profit activities will be subject to income tax at the
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preferential 10% rate pursuant to Section 27(B) thereof. (COMMISSIONER OF INTERNAL REVENUE
VS. ST. LUKES MEDICAL CENTER, INC., G.R. NO. 203514, FEBRUARY 13, 2017, J. DEL CASTILLO)

As to whether SLMC is liable for compromise penalty under Section 248(A) of the 1997 NIRC for its
alleged failure to file its quarterly income tax returns, this has also been resolved in G.R Nos. 195909
and 195960 (Commissioner of Internal Revenue v. St. Luke's Medical Center, Inc.), where the
imposition of surcharges and interest under Sections 248 and 249 of the 1997 NIRC were deleted on
the basis of good faith and honest belief on the part of SLMC that it is not subject to tax. Thus,
following the ruling of the Court in the said case, SLMC is not liable to pay compromise penalty under
Section 248(A) of the 1997 NIRC. (COMMISSIONER OF INTERNAL REVENUE VS. ST. LUKES
MEDICAL CENTER, INC., G.R. NO. 203514, FEBRUARY 13, 2017, J. DEL CASTILLO)

While the Court agrees with the CIR that the payment confirmation from the BIR presented by SLMC
is not a competent proof of payment as it does not indicate the specific taxable period the said
payment covers, the Court finds that the Certification issued by the Large Taxpayers Service of the
BIR dated May 27, 2013, and the letter from the BIR dated November 26, 2013 with attached
Certification of Payment and application for abatement are sufficient to prove payment especially
since CIR never questioned the authenticity of these documents. In fact, in a related case, G.R. No.
200688, entitled Commissioner of Internal Revenue v. St. Luke's Medical Center, lnc., the Court
dismissed the petition based on a letter issued by CIR confirming SLMC's payment of taxes, which is
the same letter submitted by SLMC in the instant case. (COMMISSIONER OF INTERNAL REVENUE
VS. ST. LUKES MEDICAL CENTER, INC., G.R. NO. 203514, FEBRUARY 13, 2017, J. DEL CASTILLO)

In sum, R.A. 9504, like R.A. 7167 in Umali, was a piece of social legislation clearly intended to afford
immediate tax relief to individual taxpayers, particularly low-income compensation earners. Indeed,
if R.A. 9504 was to take effect beginning taxable year 2009 or half of the year 2008 only, then the
intent of Congress to address the increase in the cost of living in 2008 would have been negated.
Therefore, following Umali, the test is whether the new set of personal and additional exemptions
was available at the time of the filing of the income tax return. In other words, while the status of the
individual taxpayers is determined at the close of the taxable year, their personal and additional
exemptions - and consequently the computation of their taxable income - are reckoned when the tax
becomes due, and not while the income is being earned or received. The NIRC is clear on these
matters. The taxable income of an individual taxpayer shall be computed on the basis of the calendar
year. The taxpayer is required to file an income tax return on the 15th of April of each year covering
income of the preceding taxable year. The tax due thereon shall be paid at the time the return is filed.
It stands to reason that the new set of personal and additional exemptions, adjusted as a form of
social legislation to address the prevailing poverty threshold, should be given effect at the most
opportune time as the Court ruled in Umali. (JAIME N. SORIANO VS. SECRETARY OF FINANCE AND
THE COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 184450, JANUARY 24, 2017, C.J.
SERENO.)

A clarification is proper at this point. Our ruling that the MWE exemption is available for the entire
taxable year 2008 is premised on the fact of one's status as an MWE; that is, whether the employee
during the entire year of 2008 was an MWE as defined by R.A. 9504. When the wages received exceed
the minimum wage anytime during the taxable year, the employee necessarily loses the MWE
qualification. Therefore, wages become taxable as the employee ceased to be an MWE. But the
exemption of the employee from tax on the income previously earned as an MWE remains. As the
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exemption is based on the employee's status as an MWE, the operative phrase is when the employee
ceases to be an MWE. Even beyond 2008, it is therefore possible for one employee to be exempt early
in the year for being an MWE for that period, and subsequently become taxable in the middle of the
same year with respect to the compensation income, as when the pay is increased higher than the
minimum wage. The improvement of one's lot, however, cannot justly operate to make the employee
liable for tax on the income earned as an MWE. Additionally, on the question of whether one who
ceases to be an MWE may still be entitled to the personal and additional exemptions, the answer must
necessarily be yes. The MWE exemption is separate and distinct from the personal and additional
exemptions. One's status as an MWE does not preclude enjoyment of the personal and additional
exemptions. Thus, when one is an MWE during a part of the year and later earns higher than the
minimum wage and becomes a non-MWE, only earnings for that period when one is a non-MWE is
subject to tax. It also necessarily follows that such an employee is entitled to the personal and
additional exemptions that any individual taxpayer with taxable gross income is entitled. A different
interpretation will actually render the MWE exemption a totally oppressive legislation. It would be a
total absurdity to disqualify an MWE from enjoying as much as P150,000 in personal and additional
exemptions just because sometime in the year, he or she ceases to be an MWE by earning a little more
in wages. Laws cannot be interpreted with such absurd and unjust outcome. It is axiomatic that the
legislature is assumed to intend right and equity in the laws it passes. Critical, therefore, is how an
employee ceases to become an MWE and thus ceases to be entitled to an MWE's exemption. In sum,
the proper interpretation of R.A. 9504 is that it imposes taxes only on the taxable income received in
excess of the minimum wage, but the MWEs will not lose their exemption as such. Workers who
receive the statutory minimum wage their basic pay remain MWEs. The receipt of any other income
during the year does not disqualify them as MWEs. They remain MWEs, entitled to exemption as such,
but the taxable income they receive other than as MWEs may be subjected to appropriate taxes.
(JAIME N. SORIANO VS. SECRETARY OF FINANCE AND THE COMMISSIONER OF INTERNAL
REVENUE, G.R. NO. 184450, JANUARY 24, 2017, C.J. SERENO)

Section 1 of R.A. No. 9337, amending Section 27(c) of R.A. No. 8424, by excluding petitioner from the
enumeration of GOCCs exempted from corporate income tax, is valid and constitutional. In addition,
we hold that: 1)Petitioners tax privilege of paying five percent (5%) franchise tax in lieu of all other
taxes with respect to its income from gaming operations, pursuant to P.D. 1869, as amended, is not
repealed or amended by Section 1(c) of R.A. No. 9337; 2)Petitioners income from gaming operations
is subject to the five percent (5%) franchise tax only; and 3)Petitioners income from other related
services is subject to corporate income tax only. (PHILIPPINE AMUSEMENT AND GAMING
CORPORATION VS. THE BUREAU OF INTERNAL REVENUE, G.R. NO. 215427, DECEMBER 10,
2014, J. PERALTA)

DOCUMENTARY STAMP TAX/ CAPITAL GAINS TAX

The maturity of PNB's interbank call loans was irrelevant in determining its DST liability for taxable
year 1997, relation to which the applicable law was the National Internal Revenue Code of 1977
(1977 NIRC), as amended by Presidential Decree No. 195916 and Republic Act No. 7660. Section 180
of the 1977 NIRC provides that the DST of P0.30 on each P200.00, or fractional part thereof, shall
only be imposed on the face value of: (1) loan agreements; (2) bills of exchange; (3) drafts; (4)
instruments and securities issued by the Government or any of its instrumentalities; (5) certificates
of deposits drawing interest; (6) orders for the payment of any sum of money otherwise than at sight
or on demand; and (7) promissory notes, whether negotiable or non-negotiable, except bank notes
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issued for circulation, and on each renewal of any such note. Interbank call loans, although not
considered as deposit substitutes, are not expressly included among the taxable instruments listed
in Section 180; hence, they may not be held as taxable. The five-day maturity of interbank call loans
came to be introduced only by Section 22(y) of the National Internal Revenue Code of 1997 (1997
NIRC). The provisions of the 1997 NIRC cannot be given retrospective effect to the prejudice of PNB.
This is because tax laws are prospective in application, unless their retroactive application is
expressly provided. (COMMISSIONER OF INTERNAL REVENUE vs. PHILIPPINE NATIONAL BANK,
G.R. No. 195147, JULY 11, 2016, J. BERSAMIN)

The payment of the DST and the filing of the DST Declaration Return upon loading/reloading of the
DS metering machine must not be considered as the "date of payment" when the prescriptive period
to file a claim for a refund/credit must commence. For DS metering machine users, the payment of
the DST upon loading/reloading is merely an advance payment for future application. The liability
for the payment of the DST falls due only upon the occurrence of a taxable transaction. Therefore, it
is only then that payment may be considered for the purpose of filing a claim for a refund or tax credit.
Since actual payment was already made upon loading/reloading of the DS metering machine and the
filing of the DST Declaration Return, the date of imprinting the documentary stamp on the taxable
document must be considered as the date of payment contemplated under Section 229 of the NIRC.
(PHILIPPINE BANK OF COMMUNICATIONS VS. COMMISSIONER OF INTERNAL REVENUE, G.R.
NO. 194065, JUNE 20, 2016, C.J. SERENO)

A perusal of the subject provision would clearly show it pertains only to sale transactions where real
property is conveyed to a purchaser for a consideration. The phrase granted, assigned, transferred
or otherwise conveyed is qualified by the word sold which means that documentary stamp tax
under Section 196 is imposed on the transfer of realty by way of sale and does not apply to all
conveyances of real property. Indeed, as correctly noted by the respondent, the fact that Section 196
refers to words sold, purchaser and consideration undoubtedly leads to the conclusion that only
sales of real property are contemplated therein. (COMMISSIONER OF INTERNAL REVENUE VS. LA
TONDENA DISTILLERS, INC. (LTDI) [NOW GINEBRA SAN MIGUEL], G.R. NO. 175188, JULY 15,
2015)

Capital gains is a tax on passive income, it is the seller, not the buyer, who generally would shoulder
the tax. As a general rule, therefore, any of the parties to a transaction shall be liable for the full
amount of the documentary stamp tax due, unless they agree among themselves on who shall be
liable for the same. In this case, with respect to the capital gains tax, we find merit in petitioners
posture that pursuant to Sections 24(D) and 56(A)(3) of the 1997 National Internal Revenue Code
(NIRC), capital gains tax due on the sale of real property is a liability for the account of the seller. It
has been held that since capital gains is a tax on passive income, it is the seller, not the buyer, who
generally would shoulder the tax. Also, there is no agreement as to the party liable for the
documentary stamp tax due on the sale of the land to be expropriated. But while DPWH rejects any
liability for the same, this Court must take note of petitioners Citizens Charter, which functions as a
guide for the procedure to be taken by the DPWH in acquiring real property through expropriation
under RA 8974. The Citizens Charter, issued by DPWH itself on December 4, 2013, explicitly
provides that the documentary stamp tax, transfer tax, and registration fee due on the transfer of the
title of land in the name of the Republic shall be shouldered by the implementing agency of the DPWH,
while the capital gains tax shall be paid by the affected property owner. (REPUBLIC OF THE
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PHILIPPINES, REPRESENTED BY THE DEPARTMENT OF PUBLIC WORKS AND HIGHWAYS VS.
ARLENE R. SORIANO, G.R. NO. 211666, FEBRUARY 25, 2015, J. PERALTA)

It should be noted that a DST is in the nature of an excise tax because it is imposed upon the privilege,
opportunity or facility offered at exchanges for the transaction of the business. DST is a tax on
documents, instruments, loan agreements, and papers evidencing the acceptance, assignment, or
transfer of an obligation, right or property incident thereto. DST is thus imposed on the exercise of
these privileges through the execution of specific instruments, independently of the legal status of
the transactions giving rise thereto. The transfer of real properties from SPPC to PSPC is not subject
to DST considering that the same was not conveyed to or vested in PSPC by means of any specific
deed, instrument or writing. There was no deed of assignment and transfer separately executed by
the parties for the conveyance of the real properties. The conveyance of real properties not being
embodied in a separate instrument but is incorporated in the merger plan, thus, PSPC is not liable to
pay DST. Notably, R.A. No. 9243, entitled An Act Rationalizing the Provisions of the Documentary
Stamp Tax of the National Internal Revenue Code of 1997 was enacted and took effect on April 27,
2004, which exempts the transfer of real property of a corporation, which is a party to the merger or
consolidation, to another corporation, which is also a party to the merger or consolidation, from the
payment of DST. (COMMISSIONER OF INTERNAL REVENUE VS. PILIPINAS SHELL PETROLEUM
CORPORATION, G.R. NO. 192398, SEPTEMBER 29, 2014, J. VILLARAMA, JR.)

HSBC issued SWIFT messages to its clients containing instructions about their accounts. HSBC paid
DST on the said messages. However, later on, HSBC filed for tax refund for the DST it paid. CIR denied
their claim. On review with the Supreme Court, it held that an electronic message containing
instructions to debit their respective local or foreign currency accounts in the Philippines and pay a
certain named recipient also residing in the Philippines is not transaction contemplated under
Section 181 of the Tax Code. They are also not bills of exchange due to their non-negotiability. Hence,
they are not subject to DST. (THE HONGKONG AND SHANGHAI BANKING CORPORATION
LIMITED-PHILIPPINE BRANCHES VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO.
166018 & 167728, JUNE 4, 2014, J. LEONARDO-DE CASTRO)

FRANCHISE TAX

The amendment of the 1997 NIRC, in connection with Section 22 of R.A. 9337 abolished the franchise
tax on domestic airlines and subjected PAL and similar entities to corporate income tax and value-
added tax (VAT). PAL nevertheless remains exempt from taxes, duties, royalties, registrations,
licenses, and other fees and charges, provided it pays corporate income tax as granted in its franchise
agreement. Accordingly, PAL is left with no other option but to pay its basic corporate income tax,
the payment of which shall be in lieu of all other taxes, except VAT, and subject to certain conditions
provided in its charter. In this case, the CTA found that PAL had paid basic corporate income tax for
fiscal year ending 31 March 2006. Consequently, PAL may now claim exemption from taxes, duties,
charges, royalties, or fees due on all importations of its commissary and catering supplies, provided
it shows that 1) such articles or supplies or materials are imported for use in its transport and non-
transport operations and other activities incidental thereto; and 2) they are not locally available in
reasonable quantity, quality, or price. (REPUBLIC OF THE PHILIPPINES, REP. BY THE
COMMISSIONER OF CUSTOMS VS. PHILIPPINE AIRLINES, INC. (PAL) / COMMISSIONER OF
INTERNAL REVENUE VS. PHILIPPINE AIRLINES, INC. (PAL), G.R. NO. 209353-54/G.R. NOS.
211733-34, JULY 6, 2015)
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A corporation that has been ordered to pay franchise tax delinquency but which facilities, including
its nationwide franchise, had been transferred to the National Transmission Corporation (TRANSCO)
by operation of law during the time of the alleged delinquency, cannot be ordered to pay as it is not
the proper party subject to the local franchise tax, the transferee being the one liable. (NATIONAL
POWER CORPORATION VS. PROVINCIAL GOVERNMENT OF BATAAN, SANGGUNIANG
PANLALAWIGAN OF BATAAN, PASTOR B. VICHUACO (IN HIS OFFICIAL CAPACITY AS
PROVINCIAL TREASURER OF BATAAN) AND THE REGISTER OF DEEDS OF THE PROVINCE OF
BATAAN, G.R. NO. 180654, APRIL 21, 2014, J. ABAD)

EXCISE TAX

Section 145(C) of the NIRC is clear that the excise tax on cigarettes packed by machine is imposed
per pack. "Per pack" was not given a clear definition by the NIRC. However, a "pack" would normally
refer to a number of individual components packaged as a unit. Under the same provision, cigarette
manufacturers are permitted to bundle cigarettes packed by machine in the maximum number of 20
sticks and aside from 20's, the law also allows packaging combinations of not more than 20's -it can
be 4 pouches of 5 cigarette sticks in a pack (4x5's), 2 pouches of 10 cigarette sticks in a pack (2xl0's),
etc. Based on this maximum packaging and allowable combinations, the BIR, with RA 10351 as basis,
issued RR 17-2012. The BIR also released RMC 90-2012, specifically Annex "D-1" on Cigarettes
Packed by Machine, in accordance with RA 10351 and RR 17-2012, showing in tabular form the
different brands of locally-manufactured cigarettes packed by machine with the brand names,
content/unit (pack), net retail price, and the applicable excise tax rates effective 1 January 2013. The
net retail price of some brand names was converted into individual packages of 5s or 10s pursuant
to Section 11 of RR 17-2012. xxx From the above discussion, it can be gleaned that the lawmakers
intended to impose the excise tax on every pack of cigarettes that come in 20 sticks. Individual
pouches or packaging combinations of 5's and 10's for retail purposes are allowed and will be
subjected to the same excise tax rate as long as they are bundled together by not more than 20 sticks.
Thus, by issuing Section 11 of RR 17-2012 and Annex "D-1" on Cigarettes Packed by Machine of RMC
90-2012, the BIR went beyond the express provisions of RA 10351. In this case, Section 11 of RR 17-
2012 and Annex "D-1" on Cigarettes Packed by Machine of RMC 90-2012 clearly contravened the
provisions of RA 10351. It is a well-settled principle that a revenue regulation cannot amend the law
it seeks to implement. In Commissioner of Internal Revenue v. Seagate Technology (Philippines), we
held that a mere administrative issuance, like a BIR regulation, cannot amend the law; the former
cannot purport to do any more than implement the latter. The courts will not countenance an
administrative regulation that overrides the statute it seeks to implement. In the present case, a
reading of Section 11 of RR 17-2012 and Annex "D-1" on Cigarettes Packed by Machine of RMC 90-
2012 reveals that they are not simply regulations to implement RA 10351. They are amendatory
provisions which require cigarette manufacturers to be liable to pay for more tax than the law, RA
10351, allows. The BIR, in issuing these revenue regulations, created an additional tax liability for
packaging combinations smaller than 20 cigarette sticks. In so doing, the BIR amended the law, an
act beyond the power of the BIR to do. In sum, we agree with the ruling of the RTC that Section 11 of
RR 17-2012 and Annex "D-1" on Cigarettes Packed by Machine of RMC 90-2012 are null and void.
Excise tax on cigarettes packed by machine shall be imposed on the packaging combination of 20
cigarette sticks as a whole and not to individual packaging combinations or pouches of 5's, 10's, etc.
(SECRETARY OF FINANCE CESAR V. PURISIMA VS. PHILIPPINE TOBACCO INSTITUTE, INC., GR
NO. 210251, APRIL 17, 2017, J. CARPIO)
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Lastly, as in the abovecited cases, petitioners in the present petition again raise the issue regarding
PAL's alleged failure to comply with the conditions set by Section 13 of PD 1590 for its imported
tobacco and alcohol products to be exempt from excise tax. These conditions are: (1) such supplies
are imported for the use of the franchisee in its transport/non-transport operations and other
incidental activities; and (2) they are not locally available in reasonable quantity, quality and price.
However, as this Court has previously held, the matter as to PAL's supposed noncompliance with the
conditions set by Section 13 of P.D. 1590 for its imported supplies to be exempt from excise tax, are
factual determinations that are best left to the CTA, which found that PAL had, in fact, complied with
the above conditions. (COMMISSIONER OF INTERNAL REVENUE AND COMMISSIONER OF
CUSTOMS VS. PHILIPPINE AIRLINES, INC., G.R. NO. 215705-07 FEBRUARY 22, 2017, J.
PERALTA)

Whether the Bureau of Internal Revenue may issue notices of discrepancy that effectively changes
"San Mig Light"'s classification from new brand to variant - the issues involve an application of
Section 143 of the 1997 National Internal Revenue Code (Tax Code), as amended, on the definition of
a variant, which is subject to a higher excise tax rate than a new brand. This case also applies the
requirement in Rep. Act No. 9334 that reclassification of certain fermented liquor products
introduced between January 1, 1997 and December 31, 2003 can only be done by an act of Congress.
Excise taxes are imposed on the production, sale, or consumption of specific goods. Generally, excise
taxes on domestic products are paid by the manufacturer or producer before removal of those
products from the place of production. The excise tax based on weight, volume capacity, or any other
physical unit of measurement is referred to as "specific tax." If based on selling price or other
specified value, it is referred to as "ad valorem" tax. The excise tax on beer is a specific tax based on
volume, or on a per liter basis. Before its amendment, Section 143 provided for three (3) layers of tax
rates, depending on the net retail price per liter. How a new beer product is taxed depends on its
classification, i.e. whether it is a variant of an existing brand or a new brand. Variants of a brand that
were introduced in the market after January 1, 1997 are taxed under the highest tax classification of
any variant of the brand. On the other hand, new brands are Initially classified and taxed according
to their suggested net retail price, until a survey is conducted by the Bureau of Internal Revenue to
determine their current net retail price in accordance with the specified procedure. Parenthetically,
the Bureau of Internal Revenue's actions reflect its admission and confirmation that "San Mig Light"
is a new brand. (COMMISSIONER OF INTERNAL REVENUE VS. SAN MIGUEL CORPORATION, G.R.
NOS. 205045 & 205723, JANUARY 25, 2017, J. LEONEN)

Any reclassification of fermented liquor products should be by act of Congress. Section 143 of the Tax
Code, as amended by Rep. Act No. 9334, provides for this classification freeze referred to by the
parties. In any event, petitioner's letters and Notices of Discrepancy, which effectively changed San
Mig Light's brand's classification from "new brand to variant of existing brand," necessarily changes
San Mig Light's tax bracket. Based on the legislative intent behind the classification freeze provision,
petitioner has no power to do this. A reclassification of a fermented liquor brand introduced between
January 1, 1997 and December 31, 2003, such as "San Mig Light," must be by act of Congress. There
was none in this case. A variant under the Tax Code has a technical meaning. It is determined by the
brand (name) or logo of the beer product. The variant contemplated under the tax Code has a
technical meaning. A variant is determined by the brand (name) of the beer product, whether it was
formed by prefixing or suffixing a modifier to the root name of the alleged parent brand, or whether
it carries the same logo or design. The purpose behind the definition was to properly tax brands that
Page 9 of 53

were presumed to be riding on the popularity of previously registered brands by being marketed
under an almost identical name with a prefix, suffix, or a variant. It seeks to address price differentials
employed by a manufacturer on similar products differentiated only in brand or design. Specifically,
the provision was meant to obviate any tax avoidance by manufacturing firms from the sale of lower
priced variants of its existing beer brands, thus, falling in the lower tax bracket with lower excise tax
rates. To favor government, a variant of a brand is taxed according to the highest rate of tax for that
particular brand. "San Mig Light" and "Pale Pilsen" do not share a root word. Neither is there an
existing brand in the list (Annexes C-1 and C-2 of the Tax Code) called "San Mig" to conclude that
"Light" is a suffix rendering "San Mig Light" as its "variant." As discussed in the Court of Tax Appeals
Decision, "San Mig Light" should be considered as one brand name. Respondent's statements
describing San Mig Light as a low-calorie variant is not conclusive of its classification as a variant for
excise tax purposes. Burdens are not to be imposed nor presumed to be imposed beyond the plain
and express terms of the law. "The general rule of requiring adherence to the letter in construing
statutes applies with peculiar strictness to tax laws and the provisions of a taxing act are not to be
extended by implication." Furthermore, respondent's payment of the higher taxes starting January
30, 2004 after deficiency assessments were made cannot be considered as an admission that its San
Mig Light is a variant. Section 130(A)(2) of the Tax Code requires payment of excise tax "before
removal of domestic products from place of production." These payments were made in protest as
respondent subsequently filed refund claims. Because the Bureau of Internal Revenue granted
respondent's request in its October 27, 1999 letter and confirmed this grant in its subsequent letters,
respondent cannot be faulted for relying on these actions by the Bureau of Internal Revenue. The
authority of the Bureau of Internal Revenue to overrule, correct, or reverse the mistakes or errors of
its agents is conceded. However, this authority must be exercised reasonably, i.e., only when the
action or ruling is patently erroneous or patently contrary to law. For the presumption lies in the
regularity of performance of official duty, and reasonable care has been exercised by the revenue
officer or agent in evaluating the facts before him or her prior to rendering his or her decision or
rulingin this case, prior to the approval of the registration of San Mig Light as a new brand for excise
tax purposes. A contrary view will create disorder and confusion in the operations of the Bureau of
Internal Revenue and open the administrative agency to inconsistencies in the administration and
enforcement of tax laws. (COMMISSIONER OF INTERNAL REVENUE VS. SAN MIGUEL
CORPORATION, G.R. NOS. 205045 & 205723, JANUARY 25, 2017, J. LEONEN)

Excise tax on petroleum products is essentially a tax on property, the direct liability for which
pertains to the statutory taxpayer (i.e., manufacturer, producer or importer). Any excise tax paid by
the statutory taxpayer on petroleum products sold to any of the entities or agencies named in Section
135 of the National Internal Revenue Code (NIRC) exempt from excise tax is deemed illegal or
erroneous, and should be credited or refunded to the payor pursuant to Section 204 of the NIRC. This
is because the exemption granted under Section 135 of the NIRC must be construed in favor of the
property itself, that is, the petroleum products. (CHEVRON PHILIPPINES, INC. VS. COMMISSIONER
OF INTERNAL REVENUE G.R. NO. 210836. SEPTEMBER 1, 2015)

Stemmed leaf tobacco is subject to the specific tax under Section 141(b). It is a partially prepared
tobacco. The removal of the stem or midrib from the leaf tobacco makes the resulting stemmed leaf
tobacco a prepared or partially prepared tobacco. Since the Tax Code contained no definition of
partially prepared tobacco, then the term should be construed in its general, ordinary, and
comprehensive sense. However, importation of stemmed leaf tobacco is not included in the
exemption under Section 137. The transaction contemplated in Section 137 does not include
Page 10 of 53

importation of stemmed leaf tobacco for the reason that the law uses the word sold to describe the
transaction of transferring the raw materials from one manufacturer to another. Finally, excise taxes
are essentially taxes on property because they are levied on certain specified goods or articles
manufactured or produced in the Philippines for domestic sale or consumption or for any other
disposition, and on goods imported. In this case, there is no double taxation in the prohibited sense
despite the fact that they are paying the specific tax on the raw material and on the finished product
in which the raw material was a part, because the specific tax is imposed by explicit provisions of the
Tax Code on two different articles or products: (1) on the stemmed leaf tobacco; and (2) on cigar or
cigarette. (LA SUERTE CIGAR & CIGARETTE FACTORY VS. COURT OF APPEALS AND
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 125346, G.R. NOS. 136328-29, G.R. NO.
144942, G.R. NO. 148605, G.R. NO. 158197, G.R. NO. 165499, NOVEMBER 11, 2014, J. LEONEN)

Petitioner filed the instant petition assailing the decision of the CTA finding PAL exempt from
payment of excise tax. Affirming the decision of the CTA the SC ruled that PD 1590 has not been
revoked by the NIRC of 1997, as amended. Or to be more precise, the tax privilege of PAL provided
in Sec. 13 of PD 1590 has not been revoked by Sec. 131 of the NIRC of 1997, as amended by Sec. 6 of
RA 9334. Such being the case, PAL is indeed exempt from payment of excise tax. (COMMISSIONER
OF INTERNAL REVENUE AND COMMISSIONER OF CUSTOMS VS. PHILIPPINE AIRLINES, INC., G.R.
NOS. 212536-37, AUGUST 27, 2014, J. VELASCO, JR.)

FINAL WITHHOLDING TAX

Should there have been a simultaneous sale to 20 or more lenders/investors, the Poverty Eradication
and Alleviation Certificates or the PEACe Bonds are deemed deposit substitutes within the meaning
of Sec. 22(Y) of the 1997 NIRC and RCBC Capital would have been obliged to pay the 20% FWT on
the interest or discount from the PEACe Bonds. Further, the obligation to withhold the 20% final tax
on the corresponding interest from the PEACe Bonds would likewise be required of any
lender/investor had the latter turned around and sold said PEACe Bonds, whether in whole or part,
simultaneously to 20 or more lenders or investors. The Court notes, however, that under Section 24
of the 1997 NIRC, interest income received by individuals from long-term deposits or investments
with a holding period of not less than five (5) years is exempt from the final tax. Thus, should the
PEACe Bonds be found to be within the coverage of deposit substitutes, the proper procedure was
for the Bureau of Treasury to pay the face value of the PEACe Bonds to the bondholders and for the
BIR to collect the unpaid FWT directly from RCBC Capital, or any lender or investor if such be the
case, as the withholding agents. (BANCO DE ORO, ET AL. VS. REPUBLIC OF THE PHILIPPINES, ET
AL., G.R. NO. 198756, JANUARY 13, 2015, J. LEONEN)

VALUE- ADDED TAX

The amounts earmarked and eventually paid by MEDICARD to the medical service providers do not
form part of gross receipts for VAT purposes. Since an HMO like MEDICARD is primarily engaged in
arranging for coverage or designated managed care services that are needed by plan
holders/members for fixed prepaid membership fees and for a specified period of time, then
MEDICARD is principally engaged in the sale of services. Its VAT base and corresponding liability is,
thus, determined under Section 108(A) of the Tax Code, as amended by Republic Act No. 9337. What
applies to MEDICARD is the definition of gross receipts of an HMO under RR No. 16-2005 and not the
modified definition of gross receipts in general under the RR No. 4-2007. Xxx In the proceedings
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below, the nature of MEDICARD's business and the extent of the services it rendered are not seriously
disputed. As an HMO, MEDICARD primarily acts as an intermediary between the purchaser of
healthcare services (its members) and the healthcare providers doctors, hospitals and clinics for a
fee. By enrolling membership with MEDICARD, its members will be able to avail of the pre-arranged
medical services from its accredited healthcare providers without the necessary protocol of posting
cash bonds or deposits prior to being attended to or admitted to hospitals or clinics, especially during
emergencies, at any given time. Apart from this, MEDICARD may also directly provide medical,
hospital and laboratory services, which depends upon its member's choice. Thus, in the course of its
business as such, MEDICARD members can either avail of medical services from MEDICARD's
accredited healthcare providers or directly from MEDICARD. In the former, MEDICARD members
obviously knew that beyond the agreement to pre-arrange the healthcare needs of its members,
MEDICARD would not actually be providing the actual healthcare service. Thus, based on industry
practice, MEDICARD informs its would-be member beforehand that 80% of the amount would be
earmarked for medical utilization and only the remaining 20% comprises its service fee. In the latter
case, MEDICARD's sale of its services is exempt from VAT under Section 109(G). The CTA's ruling and
CIR's Comment have not pointed to any portion of Section 108 of the NIRC that would extend the
definition of gross receipts even to amounts that do not only pertain to the services to be performed
by another person, other than the taxpayer, but even to amounts that were indisputably utilized not
by MEDICARD itself but by the medical service providers. In Philippine Health Care Providers, Inc. v.
Commissioner of Internal Revenue, the Court adopted the principal object and purpose object in
determining whether the MEDICARD therein is engaged in the business of insurance and therefore
liable for documentary stamp tax. The Court held therein that an HMO engaged in preventive,
diagnostic and curative medical services is not engaged in the business of an insurance. In sum, the
Court said that the main difference between an HMO and an insurance company is that HMOs
undertake to provide or arrange for the provision of medical services through participating
physicians while insurance companies simply undertake to indemnify the insured for medical
expenses incurred up to a pre-agreed limit. In the present case, the VAT is a tax on the value added
by the performance of the service by the taxpayer. It is, thus, this service and the value charged
thereof by the taxpayer that is taxable under the NIRC. For this Court to subject the entire amount of
MEDICARD's gross receipts without exclusion, the authority should have been reasonably founded
on the language of the statute. That language is wanting in this case. (MEDICARD. MEDICARD
PHILIPPINES, INC. VS. COMMISSIONER OF INTERNAL REVENUE, GR NO. 222743, APRIL 5, 2017,
J. REYES)

In Visayas Geothermal Power Company v. Commissioner of Internal Revenue, the Court came up with
an outline summarizing the pronouncements in San Roque, to wit: For clarity and guidance, the Court
deems it proper to outline the rules laid down in San Roque with regard to claims for refund or tax
credit of unutilized creditable input VAT. They are as follows:

1. When to file an administrative claim with the CIR:
a. General rule
(Section 112(A) and Mirant case) Within 2 years from the close of the taxable quarter
when the sales were made.

b. Exception
Page 12 of 53

(Atlas case) Within 2 years from the date of payment of the output VAT, if the
administrative claim was filed from June 8, 2007 (promulgation of Atlas) to September 12,
2008 (promulgation of Mirant).

2. When to file a judicial claim with the CTA:
a. General rule
Section 112(D); not Section 229
i. Within 30 days from the full or partial denial of the administrative claim by the CIR;
or
ii. Within 30 days from the expiration of the 120-day period provided to the CIR to
decide on the claim.

This is mandatory and jurisdictional beginning January 1, 1998 (effectivity of 1997 NIRC).

b. Exception
BIR Ruling No. DA-489-03.

The judicial claim need not await the expiration of the 120-day period, if such was filed from
December 10, 2003(issuance of BIR Ruling No. DA-489-03) to October 6, 2010 (promulgation of
Aichi). (SITEL PHILIPPINES CORPORATION (FORMERLY CLIENTLOGIC PHILS., INC.), VS. CIR, GR
NO. 201326, FEB 8, 2017, J. CAGUIOA)

In Burmeister, the Court clarified that an essential condition to qualify for zero-rating under the
aforequoted provision is that the service-recipient must be doing business outside the Philippines.
Following Burmeister, the Court, in Accenture, Inc. v. Commissioner of Internal Revenue, (Accenture),
emphasized that a taxpayer claiming for a VAT refund or credit under Section 108(B) has the burden
to prove not only that the recipient of the service is a foreign corporation, but also that said
corporation is doing business outside the Philippines. (SITEL PHILIPPINES CORPORATION
(FORMERLY CLIENTLOGIC PHILS., INC.), VS. CIR, GR NO. 201326, FEB 8, 2017, J. CAGUIOA)

The CTA Division also did not err when it denied the amount of P2,668,852.55, allegedly representing
input taxes claimed on Sitel's domestic purchases of goods and services which are supported by
invoices/receipts with pre-printed TIN-V. In Western Mindanao Power Corp. v. Commissioner of
Internal Revenue, the Court ruled that in a claim for tax refund or tax credit, the applicant must prove
not only entitlement to the grant of the claim under substantive law, he must also show satisfaction
of all the documentary and evidentiary requirements for an administrative claim for a refund or tax
credit and compliance with the invoicing and accounting requirements mandated by the NIRC, as
well as by revenue regulations implementing them. The NIRC requires that the creditable input VAT
should be evidenced by a VAT invoice or official receipt, which may only be considered as such when
the TIN-VAT is printed thereon, as required by Section 4.108-1 of RR 7-95. In the same vein,
considering that the subject invoice/official receipts are not imprinted with the taxpayer's TIN
followed by the word VAT, these would not be considered as VAT invoices/official receipts and would
not give rise to any creditable input VAT in favor of Sitel. (SITEL PHILIPPINES CORPORATION
(FORMERLY CLIENTLOGIC PHILS., INC.), VS. CIR, GR NO. 201326, FEB 8, 2017, J. CAGUIOA)

For internal revenue purposes, the sale of raw cane sugar is exempt from VAT because it is considered
to be in its original state. On the other hand, refined sugar is an agricultural product that can no longer
Page 13 of 53

be considered to be in its original state because it has undergone the refining process; its sale is thus
subject to VAT. Although the sale of refined sugar is generally subject to VAT, such transaction may
nevertheless qualify as a VAT-exempt transaction if the sale is made by a cooperative. Under Section
109(1) of the NIRC, sales by agricultural cooperatives are exempt from VAT provided the following
conditions concur, viz:

First, the seller must be an agricultural cooperative duly registered with the CDA. An agricultural
cooperative is "duly registered" when it has been issued a certificate of registration by the CDA. This
certificate is conclusive evidence of its registration.
Second, the cooperative must sell either:
1) exclusively to its members; or
2) to both members and non-members, its produce, whether in its original state or processed form.

UCSFA-MPC satisfies these two requisites. (COMMISSIONER OF INTERNAL REVENUE VS. UNITED
CADIZ SUGAR FARMERS ASSOCIATION MULTI-PURPOSE COOPERATIVE, G.R. NO. 209776,
DECEMBER 7, 2016, J. BRION)

Subsequent to the Aichi ruling and during the pendency of the case at bar, the Supreme Court En Banc
resolved the consolidated cases involved in Commissioner of Internal Revenue vs. San Roque Power
and stated that a judicial claim for refund of input VAT which was filed with the CTA before the lapse
of the 120-day period under Section 112 of the NIRC is considered to have been timely made, if such
filing occurred after the issuance of the Bureau of Internal Revenue (BIR) Ruling No. DA-489-03 dated
December 10, 2003 but before the adoption of the Aichi doctrine which was promulgated on October
6, 2010. It is undisputed that the date of filing in the case at bar falls within the period following the
issuance of BIR Ruling No. DA-489-03 on December 10, 2003 but before the promulgation of the Aichi
case on October 6, 2010. In accordance with the doctrine laid down in San Roque, we rule that
petitioner's judicial claim had been timely filed and should be given due course and consideration by
the CTA. (DEUTSCHE KNOWLEDGE SERVICES PTE. LTD. VS. COMMISSIONER OF INTERNAL
REVENUE, G.R. NO. 197980, DECEMBER 1, 2016, J. LEONARDO-DE CASTRO)

The CTA did not err in denying the claim for refund on the ground that the petitioner had not
established its zero-rated sales of services to PIATCO through the presentation of official receipts. In
this regard, as evidence of an administrative claim for tax refund or tax credit, there is a certain
distinction between a receipt and an invoice. Section 113 of the NIRC of 1997 provides that a VAT
invoice is necessary for every sale, barter or exchange of goods or properties, while a VAT official
receipt properly pertains to every lease of goods or properties; as well as to every sale, barter or
exchange of services. A "sales or commercial invoice" is a written account of goods sold or services
rendered indicating the prices charged therefor or a list by whatever name it is known which is used
in the ordinary course of business evidencing sale and transfer or agreement to sell or transfer goods
and services. A "receipt" on the other hand is a written acknowledgment of the fact of payment in
money or other settlement between seller and buyer of goods, debtor or creditor, or person
rendering services and client or customer. A VAT invoice is the seller's best proof of the sale of goods
or services to the buyer, while a VAT receipt is the buyer's best evidence of the payment of goods or
services received from the seller. A VAT invoice and a VAT receipt should not be confused and made
to refer to one and the same thing. Certainly, neither does the law intend the two to be used
alternatively. The petitioner submitted sales invoices, not official receipts, to support its claim for
refund. In light of the aforestated distinction between a receipt and an invoice, the submissions were
Page 14 of 53

inadequate for the purpose thereby intended. The mere fact that an application for zero rating has
been approved by the CIR does not, by itself, justify the grant of a refund or tax credit. The taxpayer
claiming the refund must further comply with the invoicing and accounting requirements mandated
by the NIRC, as well as by revenue regulations implementing them. (TAKENAKA CORPORATION
PHILIPPINE BRANCH VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 193321, OCTOBER
19, 2016, J. BERSAMIN)

The failure to indicate the words zero-rated on the invoices and receipts issued by a taxpayer would
result in the denial of the claim for refund or tax credit. The Court has consistently ruled on the denial
of a claim for refund or tax credit whenever the word zero-rated has been omitted on the invoices
or sale receipts of the taxpayer-claimant. Furthermore, the CTA is a highly specialized court dedicated
exclusively to the study and consideration of revenue-related problems, in which it has necessarily
developed an expertise. Hence, its factual findings, when supported by substantial evidence, will not
be disturbed on appeal. (EASTERN TELECOMMUNICATIONS PHILIPPINES, INC., VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 183531, MARCH 25, 2015, J. REYES)

Cargill filed two claims for refund. However, the court ruled that the rule must therefore be that
during the period December 10, 2003 (when BIR Ruling No. DA-489-03 was issued) to October 6,
2010 (when the Aichi case was promulgated), taxpayers-claimants need not observe the 120-day
period before it could file a judicial claim for refund of excess input VAT before the CTA. Before and
after the aforementioned period (i.e., December 10, 2003 to October 6, 2010), the observance of the
120-day period is mandatory and jurisdictional to the filing of such claim. (CARGILL PHILIPPINES,
INC VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 203774, MARCH 11, 2015, J. PERLAS-
BERNABE)

This Court has consistently held as fatal the failure to print the word zero-rated on the VAT invoices
or official receipts in claims for a refund or credit of input VAT on zero-rated sales, even if the claims
were made prior to the effectivity of R.A. 9337. As to the sufficiency of a Northern Mindanaos
company invoice to prove the sales of services to NPC, the Court finds that this claim is without
sufficient legal basis. A VAT invoice is the sellers best proof of the sale of goods or services to the
buyer, while a VAT receipt is the buyers best evidence of the payment of goods or services received
from the seller. The requirement of imprinting the word zero-rated proceeds from the rule-making
authority granted to the Secretary of Finance by the NIRC for the efficient enforcement of the same
Tax Code and its amendments. A VAT-registered person whose sales are zero-rated or effectively
zero-rated, Section 112(A) specifically provides for a two-year prescriptive period after the close of
the taxable quarter when the sales were made within which such taxpayer may apply for the issuance
of a tax credit certificate or refund of creditable input tax. (NORTHERN MINDANAO POWER
CORPORATION VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 185115, FEBRUARY 18,
2015, CJ. SERENO)

Section 112(C) of the 1997 Tax Code states the time requirements for filing a judicial claim for the
refund or tax credit of input VAT. The legal provision speaks of two periods: the period of 120 days,
which serves as a waiting period to give time for the CIR to act on the administrative claim for a
refund or credit; and the period of 30 days, which refers to the period for filing a judicial claim with
the CTA. It is the 30-day period that is at issue in this case. (ROHM APOLLO SEMICONDUCTOR
PHILIPPINES VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 168950, JANUARY 14, 2015,
C.J. SERENO)
Page 15 of 53

Its petition for review having been denied by the CTA for being prematurely filed, petitioner filed the
instant petition arguing that since it filed its judicial claim after the issuance of BIR Ruling No. DA-
489-03, but before the adoption of the Aichi doctrine, it can invoke the said BIR Ruling. The SC ruled
that the jurisdiction of the CTA over decisions or inaction of the CIR is only appellate in nature and,
thus, necessarily requires the prior filing of an administrative case before the CIR under Section 112.
A petition filed prior to the lapse of the 120-day period prescribed under said Section would be
premature for violating the doctrine on the exhaustion of administrative remedies. There is,
however, an exception to the mandatory and jurisdictional nature of the 120+30 day period. The
Court in San Roque noted that BIR Ruling No. DA-489-03, dated December 10, 2003, expressly stated
that the "taxpayer-claimant need not wait for the lapse of the 120-day period before it could seek
judicial relief with the CTA by way of Petition for Review." Hence, taxpayers can rely on BIR Ruling
No. DA-489-03 from the time of its issuance on December 10, 2003 up to its reversal by this Court in
Aichi on October 6, 2010, where it was held that the 120+30 day period was mandatory and
jurisdictional. (TAGANITO MINING CORPORATION VS. COMMISSIONER OF INTERNAL REVENUE,
G.R. NO. 201195, NOVEMBER 26, 2014, J. MENDOZA)

CE Luzon filed an action for refund of the VAT. The court ruled that While both claims for refund were
filed within the two (2)-year prescriptive period, CE Luzon failed to comply with the 120-day period
as it filed its judicial claim in C.T.A. Case No. 6792 four (4) days after the filing of the administrative
claim, while in C.T.A. Case No. 6837, the judicial claim was filed a day after the filing of the
administrative claim. Proceeding from the aforementioned jurisprudence, only C.T.A. Case No. 6792
should be dismissed on the ground of lack of jurisdiction for being prematurely filed. In contrast, CE
Luzon filed its administrative and judicial claims for refund in C.T.A. Case No. 6837 during the period,
i.e., from December 10, 2003 to October 6, 2010, when BIR Ruling No. DA-489-03 was in place. As
such, the aforementioned rule on equitable estoppel operates in its favor, thereby shielding it from
any supposed jurisdictional defect which would have attended the filing of its judicial claim before
the expiration of the 120-day period. (COMMISSIONER OF INTERNAL REVENUE VS. CE LUZON
GEOTHERMAL POWER COMPANY, INC., G.R. NO. 190198, SEPTEMBER 17, 2014, J. PERLAS-
BERNABE)

Section 112(A) and (C) must be interpreted according to its clear, plain, and unequivocal language.
The taxpayer can file his administrative claim for refund or credit at anytime within the two-year
prescriptive period. If he files his claim on the last day of the two-year prescriptive period, his claim
is still filed on time. The Commissioner will have 120 days from such filing to decide the claim. If the
Commissioner decides the claim on the 120th day, or does not decide it on that day, the taxpayer still
has 30 days to file his judicial claim with the CTA. This is not only the plain meaning but also the only
logical interpretation of Section 112(A) and (C). (SAN ROQUE POWER CORPORATION VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 205543, JUNE 30, 2014, J. LEONARDO-DE
CASTRO)
The 2-year period under Section 229 does not apply to appeals before the CTA in relation to claims
for a refund or tax credit for unutilized creditable input VAT. Section 229 pertains to the recovery of
taxes erroneously, illegally, or excessively collected. San Roque stressed that input VAT is not
excessively collected as understood under Section 229 because, at the time the input VAT is
collected, the amount paid is correct and proper. It is, therefore, Section 112 which applies
specifically with regard to claiming a refund or tax credit for unutilized creditable input VAT.
Page 16 of 53

(VISAYAS GEOTHERMAL POWER COMPANY VS. COMMISSIONER OF INTERNAL REVENUE, G.R.
NO. 197525, JUNE 4, 2014, J. MENDOZA)

A claim for tax refund or credit, like a claim for tax refund exemption, is construed strictly against the
taxpayer. One of the conditions for a judicial claim of refund or credit under the VAT System is
compliance with the 120+30 day mandatory and jurisdictional periods. Thus, strict compliance with
the 120+30 day periods is necessary for such a claim to prosper, whether before, during, or after the
effectivity of the Atlas doctrine, except for the period from the issuance of BIR Ruling No. DA-489-03
on 10 December 2003 to 6 October 2010 when the Aichi doctrine was adopted, which again
reinstated the 120+30 day periods as mandatory and jurisdictional. (MIRAMAR FISH COMPANY,
INC., VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 185432, JUNE 4, 2014, J. PEREZ)

LOCAL TAXATION

Section 137 of Republic Act No. 7160 (the Local Government Code of 1991) is categorical in stating
that franchise tax can only be imposed on businesses enjoying a franchise. This goes without saying
that without a franchise, a local government unit cannot impose franchise tax. Indeed, the enactment
of EPIRA separated the transmission and sub-transmission functions of the state-owned Napocor
from its generation function, and transferred all its transmission assets to the then newly-created
TRANSCO, which was wholly owned by PSALM Corporation at that time. Power generation is no
longer considered a public utility operation, and companies which shall engage in power generation
and supply of electricity are no longer required to secure a national franchise. This is expressly
provided under Section 6 of EPIRA. EPIRA effectively removed power generation from the ambit of
local franchise taxes. Hence, as regards Napocor's business of generating electricity, the franchise
taxes sought to be collected by the Provincial Government of Bataan for the latter part of 2001 up to
2003 are devoid of any statutory basis. As regards Napocor's electric transmission function, under
Section 8 of the same law, all transmission assets of Napocor were to be transferred to TRANSCO
within six (6) months from the effectivity of EPIRA, or by December 26, 2001. Hence, until the
transfer date of the transmission assets, which by express provision of EPIRA shall not be later than
December 26, 2001, these assets, as well as the franchise, belong to and are operated by Napocor,
and the latter is consequently subject to the local franchise tax. (NATIONAL POWER CORPORATION
VS. PROVINCIAL GOVERNMENT OF BATAAN, GR 180654, MARCH 6, 2017, J. LEONEN)

Under Section 187 of the Local Government Code of 1991, aggrieved taxpayers who question the
validity or legality of a tax ordinance are required to file an appeal before the Secretary of Justice
before they seek intervention from the regular courts. In Reyes v. Court of Appeals, this Court
declared the mandatory nature of Section 187 of the Local Government Code of 1991. The doctrine
of exhaustion of administrative remedies, like the doctrine on hierarchy of courts, is not an iron-clad
rule. It admits of several well-defined exceptions. In Alta Vista Golf and Country Club v. City of Cebu,
this Court excluded the case from the strict application of the principle on exhaustion of
administrative remedies, particularly for non-compliance with Section 187 of the Local Government
Code of 1991, on the ground that the issue raised in the Petition was purely legal. In this case,
however, the issues involved are not purely legal. There are factual issues that need to be addressed
for the proper disposition of the case. In other words, this case is still not ripe for adjudication. To
question the validity of the ordinance, petitioners should have first filed an appeal before the
Secretary of Justice. (CRISANTO M. AALA VS. HON. REY T. UY, G.R. NO. 202781, JANUARY 10,
2017, J. LEONEN)
Page 17 of 53

Under Section 166 of the Local Government Code of 1991, local taxes "shall accrue on the first (1st)
day of January of each year. When the questioned ordinance was published in July 2012, the City
Government of Tagum could not have immediately issued real property tax assessments. Hence,
petitioners had ample time within which to question the validity of the tax ordinance. In cases where
the validity or legality of a tax ordinance is questioned, the rule that real property taxes must first be
paid before a protest is lodged does not apply. Taxpayers must first receive an assessment before this
rule is triggered. In Jardine, this Court ruled that prior payment under protest is not required >>
when the taxpayer is questioning the very authority of the assessor to impose taxes. Hence, if a
taxpayer disputes the reasonableness of an increase in a real estate tax assessment, he is required to
"first pay the tax" under protest. Otherwise, the city or municipal treasurer will not act on his protest.
In the case at bench, however, the petitioners are questioning the very authority and power of the
assessor, acting solely and independently, to impose the assessment and of the treasurer to collect
the tax. These are not questions merely of amounts of the increase in the tax but attacks on the very
validity of any increase. (CRISANTO M. AALA VS. HON. REY T. UY, G.R. NO. 202781, JANUARY 10,
2017, J. LEONEN)

Settled is the rule that should the taxpayer/real property owner question the excessiveness or
reasonableness of the assessment, Section 252 of the LGC of 1991 directs that the taxpayer should
first pay the tax due before his protest can be entertained. There shall be annotated on the tax receipts
the words "paid under protest." It is only after the taxpayer has paid the tax due that he may file a
protest in writing within 30 days from payment of the tax to the Provincial, City or Municipal
Treasurer, who shall decide the protest within sixty days from receipt. In no case is the local treasurer
obliged to entertain the protest unless the tax due has been paid. Moreover, as settled in
jurisprudence, a claim for exemption from the payment of real property taxes does not actually
question the assessor's authority to assess and collect such taxes, but pertains to the reasonableness
or correctness of the assessment by the local assessor. By providing that real property not declared
and proved as tax-exempt shall be included in the assessment roll, this implies that the local assessor
has the authority to assess the property for realty taxes, and any subsequent claim for exemption
shall be allowed only when sufficient proof has been adduced supporting the claim. Thus, if the
property being taxed has not been dropped from the assessment roll, taxes must be paid under
protest if the exemption from taxation is insisted upon. Finally, while it is evident in jurisprudence
that the filing of motion for reconsideration before the LBAA is allowed, this Court finds that,
inevitably, the filing of the appeal before the CBAA through registered mail on November 16, 2006
was already late. It is settled that the "fresh period rule" in the case of Domingo Neypes, et al. vs. Court
of Appeals, et al. applies only to judicial appeals and not to administrative appeals. In the instant case,
the subject appeal, i.e., appeal from a decision of the LBAA to the CBAA, is not judicial but
administrative in nature. Thus, the "fresh period rule" in Neypes does not apply. (NATIONAL POWER
CORPORATION VS. THE PROVINCIAL TREASURER OF BENGUET, THE PROVINCIAL ASSESSOR
OF BENGUET, THE MUNICIPAL TREASURER OF ITOGON, BENGUET AND THE MUNICIPAL
ASSESSOR OF ITOGON, BENGUET, G.R. NO. 209303, NOVEMBER 14, 2016, J. PERALTA)

Indisputably, the power of LGUs to impose business taxes derives from Section 143 of the LGC.
However, the same is subject to the explicit statutory impediment provided for under Section 133(h)
of the same Code which prohibits LGUs from imposing taxes, fees or charges on petroleum
products. It can, therefore, be deduced that although petroleum products are subject to excise tax,
the same is specifically excluded from the broad power granted to LGUs under Section 143(h) of the
Page 18 of 53

LGC to impose business taxes. (BATANGAS CITY, MARIA TERESA GERON, IN HER CAPACITY AS
CITY TREASURER OF BATANGAS CITY, ET AL. VS. PILIPINAS SHELL PETROLEUM
CORPORATION, G.R. NO. 187631, JULY 8, 2015)

The collections made accrue to its socialized housing programs and projects. The (socialized housing)
tax is not a pure exercise of taxing power or merely to raise revenue; it is levied with a regulatory
purpose. The levy is primarily in the exercise of the police power for the general welfare of the entire
city. As with the State, LGUs may be considered as having properly exercised their police power only
if there is a lawful subject and a lawful method or, to be precise, if the following requisites are met:
(1) the interests of the public generally, as distinguished from those of a particular class, require its
exercise and (2) the means employed are reasonably necessary for the accomplishment of the
purpose and not unduly oppressive upon individuals. (JOSE J. FERRER, JR. VS. CITY MAYOR
HERBERT BAUTISTA, CITY COUNCIL OF QUEZON CITY, CITY TREASURER OF QUEZON CITY AND
CITY ASSESSOR OF QUEZON CITY, G.R. NO. 210551, JUNE 30, 2015)

The garbage fee is not valid imposition being violative of the equal protection as the rates charged
under the ordinance are unjust and equitable. A resident of a condominium unit or socialized housing
pay twice the amount of a resident of a lot similar in size There is no substantial distinction between
an occupant of a lot and an occupant of a condominium unit, socialized housing project or apartment
as the garbage output produced by these types of occupants is uniform and does not vary to a large
degree. A similar schedule of fee would have been just and equitable. The classification is not germane
to the purpose of promoting shared responsibility. There is discrimination between occupant of a lot
and occupant of a condo unit or socialized housing project. (JOSE J. FERRER, JR. VS. CITY MAYOR
HERBERT BAUTISTA, CITY COUNCIL OF QUEZON CITY, CITY TREASURER OF QUEZON CITY AND
CITY ASSESSOR OF QUEZON CITY, G.R. NO. 210551. JUNE 30, 2015)

In the case at bar, through the application and enforcement of Sec. 14 of R.A. 9167 which earmarks
the income on amusement taxes imposed by LGUs in favor of FDCP and the producers of graded films,
the income from the amusement taxes levied by the covered LGUs did not and will under no
circumstance accrue to them, not even partially, despite being the taxing authority therefor. Congress
therefore, clearly overstepped its plenary legislative power, the amendment being violative of the
fundamental laws guarantee on local autonomy as echoed in Sec. 130(d) of the LGC which provide
that revenue collected pursuant to the said code shall inure to the benefit of the local government.
(FILM DEVELOPMENT COUNCIL OF THE PHILIPPINES VS. COLON HERITAGE REALTY
CORPORATION, OPERATOR OF ORIENTE, OPERATOR OF ORIENTE GROUP THEATERS,
REPRESENTED BY ISIDRO A. CANIZARES/FILM DEVELOPMENT COUNCIL OF THE PHILIPPINES
VS. CITY OF CEBU AND SM PRIME HOLDINGS, INC., G.R. NO. 203754/G.R. NO. 204418, JUNE 16,
2015)

In this case the Supreme Court applied to MCIAA the findings and conclusions of the Court in the
2006 MIAA case, ruling: MIAA is a government instrumentality vested with corporate powers and
performing essential public services pursuant to Section 2(10) of the Introductory Provisions of the
Administrative Code. As a government instrumentality, MIAA is not subject to any kind of tax by local
governments under Section 133(o) of the Local Government Code. The exception to the exemption
in Section 234(a) does not apply to MIAA because MIAA is not a taxable entity under the Local
Government Code. Such exception applies only if the beneficial use of real property owned by the
Page 19 of 53

Republic is given to a taxable entity. (MACTAN CEBU INTERNATIONAL AIRPORT AUTHORITY
(MCIAA) VS. CITY OF LAPU-LAPU, ET AL., G.R. NO. 181756, JUNE 15, 2015)

Setting the rate of the additional levy for the special education fund at less than 1% is within the
taxing power of local government units. It is consistent with the guiding constitutional principle of
local autonomy. It was well within the power of the Sangguniang Panlalawigan of Palawan to enact
an ordinance providing for additional levy on real property tax for the special education fund at the
rate of 0.5% rather than at 1%. (LUCENA D. DEMAALA VS. COMMISSION ON AUDIT,
REPRESENTED BY ITS CHAIRPERSON COMMISSIONER MA. GRACIA M. PULIDO TAN, G.R. NO.
199752, FEBRUARY 17, 2015, J. LEONEN)

It is already well-settled that although the power to tax is inherent in the State, the same is not true
for the LGUs to whom the power must be delegated by Congress and must be exercised within the
guidelines and limitations that Congress may provide. In the case at bar, the sanggunian of the
municipality or city cannot enact an ordinance imposing business tax on the gross receipts of
transportation contractors, persons engaged in the transportation of passengers or freight by hire,
and common carriers by air, land, or water, when said sanggunian was already specifically prohibited
from doing so. Any exception to the express prohibition under Section 133(j) of the LGC should be
just as specific and unambiguous. Section 21(B) of the Manila Revenue Code, as amended, is null and
void for being beyond the power of the City of Manila and its public officials to enact, approve, and
implement under the LGC.(CITY OF MANILA, HON. ALFREDO S. LIM, AS MAYOR OF THE CITY OF
MANILA, ET AL. VS. HON. ANGEL VALERA COLET, AS PRESIDING JUDGE, REGIONAL TRIAL
COURT OF MANILA (BR. 43), ET AL., G.R. NO. 120051, DECEMBER 10, 2014, J. LEONARDO-DE
CASTRO)

The Citys yearly imposition of the 25% surcharge, which was sustained by the trial court and the
Court of Appeals, resulted in an aggregate penalty that is way higher than NAPOCORs basic tax
liabilities. A surcharge regardless of how it is computed is already a deterrent. While it is true that
imposing a higher amount may be a more effective deterrent, it cannot be done in violation of law
and in such a way as to make it confiscatory. (NATIONAL CORPORATION POWER VS. CITY OF
CABANATUAN REPRESENTED BY ITS CITY MAYOR, HON. HONORATO PEREZ, G.R. NO. 177332,
OCTOBER 01, 2014, J. LEONEN)

REAL PROPERTY TAX

Under Section 133(n) of the Local Government Code, the taxing power of local government units shall
not extend to the levy of taxes, fees, or charges on duly registered cooperatives under the Cooperative
Code. Section 234(d) of the Local Government Code specifically provides for real property tax
exemption to cooperatives. NGPI-NGEI, as the owner of the land being leased by respondent, falls
within the purview of the law. Section 234 of the Local Government Code exempts all real property
owned by cooperatives without distinction. Nothing in the law suggests that the real property tax
exemption only applies when the property is used by the cooperative itself. Similarly, the instance
that the real property is leased to either an individual or corporation is not a ground for withdrawal
of tax exemption. This exemption benefits the cooperative's lessee. Moreover, the characterization of
machinery as real property is governed by the Local Government Code and not the Civil Code.
(PROVINCIAL ASSESSOR OF AGUSAN DEL SUR VS. FILIPINAS PALM PLANTATION, G.R. NO.
183416, OCTOBER 5, 2016, J. LEONEN)
Page 20 of 53

In disputes involving real property taxation, the general rule is to require the taxpayer to first avail
of administrative remedies and pay the tax under protest before allowing any resort to a judicial
action, except when the assessment itself is alleged to be illegal or is made without legal authority.
For example, prior resort to administrative action is required when among the issues raised is an
allegedly erroneous assessment, like when the reasonableness of the amount is challenged, while
direct court action is permitted when only the legality, power, validity or authority of the assessment
itself is in question. Stated differently, the general rule of a prerequisite recourse to administrative
remedies applies when questions of fact are raised, but the exception of direct court action is allowed
only when purely questions of law are involved. (CAPITOL WIRELESS, INC. VS. PROVINCIAL
TREASURER OF BATANGAS, GR 180110, MAY 30, 2016, PERALTA, J.)

As far as local government units are concerned, the areas described are to be considered subsumed
under the term municipal waters under the LGC. Although the term "municipal waters" appears in
the Code in the context of the grant of quarrying and fisheries privileges for a fee by local
governments, its inclusion in the Code's Book II which covers local taxation means that it may also
apply as guide in determining the territorial extent of the local authorities' power to levy real
property taxation. Thus, the jurisdiction or authority over such part of the subject submarine cable
system lying within Philippines jurisdiction includes the authority to tax the same, for taxation is one
(1) of the three (3) basic and necessary attributes of sovereignty, and such authority has been
delegated by the national legislature to the local governments with respect to real property taxation.
(CAPITOL WIRELESS, INC. VS. PROVINCIAL TREASURER OF BATANGAS, GR 180110, MAY 30,
2016, PERALTA, J.)

The burden of proving exemption from local taxation is upon whom the subject real property is
declared. Under the LGC, every person by whom or for whom real property is declared, who shall
claim tax exemption for such property from real property taxation shall file with the provincial, city,
or municipal assessor within thirty (30) days from the date of the declaration of real property
sufficient documentary evidence in support of such claim. (CAPITOL WIRELESS, INC. VS.
PROVINCIAL TREASURER OF BATANGAS, GR 180110, MAY 30, 2016, PERALTA, J.)

Being an instrumentality of the national government, the PEZA cannot be taxed by local government
units. Although a body corporate vested with some corporate powers, the PEZA is not a government-
owned or controlled corporation taxable for real property taxes. The PEZAs predecessor, the EPZA,
was declared non-profit in character with all its revenues devoted for its development, improvement,
and maintenance. Consistent with this non-profit character, the EPZA was explicitly declared exempt
from real property taxes under its charter. Even the PEZAs lands and buildings whose beneficial use
have been granted to other persons may not be taxed with real property taxes. The PEZA may only
lease its lands and buildings to PEZA-registered economic zone enterprises and entities. These PEZA-
registered enterprises and entities, which operate within economic zones, are not subject to real
property taxes. (CITY OF LAPU-LAPU VS. PHILIPPINE ECONOMIC ZONE AUTHORITY; PROVINCE
OF BATAAN, REPRESENTED BY GOVERNOR ENRIQUE T. GARCIA, JR., AND EMERLINDA S.
TALENTO, IN HER CAPACITY AS PROVINCIAL TREASURER OF BATAAN VS. PHILIPPINE
ECONOMIC ZONE AUTHORITY, G.R. NO. 184203, G.R. NO. 187583, NOVEMBER 26, 2014, J.
LEONEN)

Page 21 of 53

Here, petitioner Genato was found delinquent in the payment of his real property taxes. However, as
he duly pointed out, a simple mathematical application would show that if the assessed values in the
2nd and 3rd tax declarations were added, P4,866,350.00 and P3,831,520.00, the same would amount
to P8,697,870.00, the assessed value of the property as indicated in the original tax declaration.
Therefore, if all the tax declarations issued by respondent Pulmano refer to one and the same
property of petitioner, and the latter fully paid all its realty taxes due on the same, then it would
follow that the finding of delinquency did not have any basis. (GENATO INVESTMENTS, INC. VS.
HON. JUDGE OSCAR P. BARRIENTOS, IN HIS CAPACITY AS THE PRESIDING JUDGE OF THE
REGIONAL TRIAL COURT, OF CALOOCAN CITY, BRANCH 123, EMILY P. DIZON, IN HER
CAPACITY AS THE BRANCH CLERK OF COURT OF THE REGIONAL TRIAL COURT OF CALOOCAN
CITY, BRANCH 123, JIMMY T. SORO, COURT PROCESS SERVER OF THE REGIONAL TRIAL COURT
OF . CALOOCAN, BRANCH 123, EVELINA M. GARMA, CITY TREASURER OF CALOOCAN CITY,
PHILLIP L. YAM, OFFICER-IN-CHARGE, REAL PROPERTY TAX DIVISION OF THE CALOOCAN CITY
TREASURER'S OFFICE, ANTHONY B. PULMANO, OFFICER-IN-CHARGE, CITY ASSESSOR OF
CALOOCAN CITY, AND LAVERNE REALTY & DEVELOPMENT CORPORATION, G.R NO. 207443,
JULY 23, 2014, J. PEREZ)

The transformers, electric posts, transmission lines, insulators, and electric meters of MERALCO may
qualify as machinery under the Local Government Code subject to real property tax. MERALCO is a
public utility engaged in electric distribution, and its transformers, electric posts, transmission lines,
insulators, and electric meters constitute the physical facilities through which MERALCO delivers
electricity to its consumers. Each may be considered as one or more of the following: a machine,
equipment, contrivance, instrument, appliance, apparatus, or installation. The Court
highlights that under Section 199(o) of the Local Government Code, machinery, to be deemed real
property subject to real property tax, need no longer be annexed to the land or building as these may
or may not be attached, permanently or temporarily to the real property, and in fact, such machinery
may even be mobile. The same provision though requires that to be machinery subject to real
property tax, the physical facilities for production, installations, and appurtenant service facilities,
those which are mobile, self-powered or self-propelled, or not permanently attached to the real
property (a) must be actually, directly, and exclusively used to meet the needs of the particular
industry, business, or activity; and (2) by their very nature and purpose, are designed for, or
necessary for manufacturing, mining, logging, commercial, industrial, or agricultural purposes.
(MANILA ELECTRIC COMPANY VS. THE CITY ASSESSOR AND CITY TREASURER OF LUCENA CITY
G.R. NO. 166102. AUGUST 5, 2015)

CUSTOMS MODERNIZATION AND TARIFF ACT

*NOTE: Republic Act (RA) No. 10863, otherwise known as the Customs Modernization and Tariff
Act (CMTA), was signed into law just recently on 30 May 2016.

The law is clear and explicit. It gives a non-extendible period of 30 days for the importer to file the
entry which we have already ruled pertains to both the IED and IEIRD. Thus under Section 1801 in
relation to Section 1301, when the importer fails to file the entry within the said period, he "shall be
deemed to have renounced all his interests and property rights" to the importations and these shall
Page 22 of 53

be considered impliedly abandoned in favor of the government. It was the law itself which considered
the importation abandoned when it failed to file the IEIRDs within the allotted time. RA 7651 no
longer requires that there be other acts or omissions where an intent to abandon can be inferred. It
is enough that the importer fails to file the required import entries within the reglementary period.
Abandonment of such shipment (imported article) constitutes renouncement of all his interests and
property rights therein. With regard to the assessments, however, there being no evidence to prove
that petitioner committed fraud in belatedly filing its Import Entry and Internal Revenue Declaration
within the 30-day period prescribed under Section 1301 of the TCCP, as amended, respondent's
rights to question the propriety thereof and to collect the amount of the alleged deficiency customs
duties, more so the entire value of the subject shipment, have already prescribed. Simply put, in the
absence of fraud, the entry and corresponding payment of duties made by petitioner becomes final
and conclusive upon all parties after one (1) year from the date of the payment of duties in
accordance with Section 1603 of the TCCP, as amended. (PILIPINAS SHELL PETROLEUM
CORPORATION VS. COMMISSIONER OF CUSTOMS, G.R. NO. 195876, DECEMBER 5, 2016, J.
PEREZ)

With the cancellation of the TCCs, the tax liabilities of PSPC under the original assessments were
considered unpaid, hence BOCs demand letters and the action for collection in the RTC. To repeat,
these assessed customs duties and taxes were previously assessed and paid by the taxpayer, only
that the TCCs turned out to be spurious and hence worthless certificates that did not extinguish
PSPCs tax liabilities. (REPUBLIC OF THE PHILIPPINES, REPRESENTED BY THE BUREAU OF
CUSTOMS VS. PILIPINAS SHELL PETROLEUM CORPORATION, G.R. NO. 209324. DECEMBER 9,
2015)

In unlawful importation, also known as outright smuggling, goods and articles of commerce are
brought into the country without the required importation documents, or are disposed of in the local
market without having been cleared by the BOC or other authorized government agencies, to evade
the payment of correct taxes, duties and other charges. Such goods and articles do not undergo the
processing and clearing procedures at the BOC, and are not declared through submission of import
documents, such as the import entry and internal revenue declaration. In various fraudulent
practices against customs revenue, also known as technical smuggling, on the other hand, the goods
and articles are brought into the country through fraudulent, falsified or erroneous declarations, to
substantially reduce, if not totally avoid, the payment of correct taxes, duties and other charges. Such
goods and articles pass through the BOC, but the processing and clearing procedures are attended by
fraudulent acts in order to evade the payment of correct taxes, duties, and other charges. Often
committed by means of misclassification of the nature, quality or value of goods and articles,
undervaluation in terms of their price, quality or weight, and misdeclaration of their kind, such form
of smuggling is made possible through the involvement of the importers, the brokers and even some
customs officials and personnel. (BUREAU OF CUSTOMS VS. THE HONORABLE AGNES VST
DEVANADERA, ET AL. G.R. NO. 193253. SEPTEMBER 8, 2015)

The penalty of forfeiture could be imposed on any vessel engaged in smuggling, provided that the
following conditions were present, to wit: (1) The vessel is "used unlawfully in the importation or
exportation of articles into or from" the Philippines; (2) The articles are imported to or exported from
"any Philippine port or place, except a port of entry"; or (3) If the vessel has a capacity of less than 30
tons and is "used in the importation of articles into any Philippine port or place other than a port of
the Sulu Sea, where importation in such vessel may be authorized by the Commissioner, with the
Page 23 of 53

approval of the department head." With the absence of the first and second conditions, the M/V Don
Martin must be released. (M/V "DON MARTIN" VOY 047 AND CARGOES OF 6500 SACKS OF
IMPORTED RICE, ET AL. VS. HON. SECRETARY OF FINANCE, BUREAU OF CUSTOMS, AND THE
DISTRICT COLLECTOR OF CAGAYAN DE ORO CITY, G.R. NO. 160206. JULY 15, 2015)

NFSC, Japan-based company, sells raw sugar. However, NFSC was charged by violation of the Joint
Order by the Commissioner Customs. The court ruled that NFSC did not violate the order and such
was in good faith. The Court ruled that the onus probandi to establish the existence of fraud is lodged
with the Bureau of Customs which ordered the forfeiture of the imported goods. Fraud is never
presumed. It must be proved. Failure of proof of fraud is a bar to forfeiture. The reason is that
forfeitures are not favored in law and equity. The fraud contemplated by law must be intentional
fraud, consisting of deception willfully and deliberately done or resorted to in order to induce
another to give up some right. Absent fraud, the Bureau of Customs cannot forfeit the shipment in its
favor. (THE COMMISSIONER OF CUSTOMS & THE DISTRICT COLLECTOR OF CUSTOMS FOR THE
PORT OF ILOILO VS. NEW FRONTIER SUGAR CORPORATION, G.R. NO. 163055, JUNE 11, 2014,
J. PEREZ)

TAX REMEDIES

Taxpayers who availed themselves of the tax amnesty program are entitled to the immunities and
privileges under Section 6 of the law. This Court has declared that submission of the documentary
requirements and payment of the amnesty tax is considered full compliance with Republic Act No.
9480 and the taxpayer can immediately enjoy the immunities and privileges enumerated in Section
6 of the law. The plain and straightforward conditions were obviously meant to encourage taxpayers
to avail of the amnesty program, thereby enhancing revenue administration and collection. The Court
explained that the documentary requirements and payment of the amnesty tax operate as a
suspensive condition, such that completion of these requirements entitles the taxpayer-applicant to
immediately enjoy the immunities and privileges under Republic Act No. 9480. However, the Court
further stated that Section 6 of the law contains a resolutory condition. Immunities and privileges
will cease to apply to taxpayers who, in their SALN, were proven to have understated their net worth
by 30% or more. Thus, the amnesty granted under the law is revoked once the taxpayer is proven to
have under-declared his assets in his SALN by 30% or more. Pursuant to Section 10 of the Tax
Amnesty Law, amnesty taxpayers who wilfully understate their net worth shall not only be liable for
perjury under the Revised Penal Code, but, upon conviction, also subject to immediate tax fraud
investigation in order to collect all taxes due and to criminally prosecute for tax evasion.
(COMMISSIONER OF INTERNAL REVENUE VS. APO CEMENT CORPORATION G.R. NO.193381,
FEBRUARY 8, 2017, LEONEN, J.)

Unlike the power to compromise or abate a taxpayers liability under Section 204 of the 1997
National Internal Revenue Code that is within the discretion of respondent Commissioner of Internal
Revenue, its authority under Republic Act No. 9480 is limited to determining whether (a) the
taxpayer is qualified to avail oneself of the tax amnesty; (b) all the requirements for availment under
the law were complied with; and (c) the correct amount of amnesty tax was paid within the period
prescribed by law. There is nothing in Republic Act No. 9480 which can be construed as authority
for respondent Commissioner of Internal Revenue to introduce exceptions and/or conditions to the
coverage of the law nor to disregard its provisions and substitute his own personal judgment. (ING
BANK N.V. VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 167679. JULY 22, 2015)
Page 24 of 53

Qualified taxpayers with pending tax cases may still avail themselves of the tax amnesty program
under Republic Act No. 9480, otherwise known as the 2007 Tax Amnesty Act. Thus, the provision in
BIR Revenue Memorandum Circular No. 19-2008 excepting "issues and cases which were ruled by
any court (even without finality) in favor of the BIR prior to amnesty availment of the taxpayer" from
the benefits of the law is illegal, invalid, and null and void. The duty to withhold the tax on
compensation arises upon its accrual. (ING BANK N.V., ENGAGED IN BANKING OPERATIONS IN
THE PHILIPPINES AS ING BANK N.V. MANILA BRANCH VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 167679, JULY 22, 2015, J. LEONEN)

The parties agreed to amicably settle all cases between them involving claims for tax refund/credit,
including the instant case. A review of the whereas clauses of the Universal Compromise Agreement
reveals the various court cases filed by petitioners, including this case, for the refund and/or issuance
of tax credit covering the local business taxes payments they paid to respondent City of Manila
pursuant to Section 21 of the latters Revenue Code. In this relation, it is observed that the present
case would have been rendered moot and academic had the parties informed the Court of the UCAs
supervening execution. Be that as it may, and considering that: (a) the UCA appears to have been
executed in accordance with the requirements of a valid compromise agreement; (b) the UCA was
executed more than a year prior to the promulgation of the subject Decision; and (c) the result of
both the UCA and the subject Decision are practically identical, i.e., that petitioners are not entitled
to any tax refund/credit, the Court herein resolves to approve and adopt the pertinent terms and
conditions of the UCA insofar as they govern the settlement of the present dispute. (METRO MANILA
SHOPPING MECCA CORP., SHOEMART, INC., SM PRIME HOLDINGS, INC., STAR APPLIANCES
CENTER, SUPER VALUE, INC., ACE HARDWARE PHILIPPINES, INC., HEAL TH AND BEAUTY, INC.,
JOLLIMART PHILS. CORP.,
AND SURPLUS MARKETING CORPORATION VS. MS. LIBERTY M. TOLEDO, IN HER OFFICIAL
CAPACITY AS THE CITY TREASURER OF MANILA, AND THE CITY OF MANILA, G.R. NO. 190818.
NOVEMBER 10, 2014, J. PERLAS-BERNABE)

ASSESSMENT

The absence of an LOA violated MEDICARD's right to due process. An LOA is the authority given to
the appropriate revenue officer assigned to perform assessment functions. It empowers or enables
said revenue officer to examine the books of account and other accounting records of a taxpayer for
the purpose of collecting the correct amount of tax. An LOA is premised on the fact that the
examination of a taxpayer who has already filed his tax returns is a power that statutorily belongs
only to the CIR himself or his duly authorized representatives. Based on Section 6 of the NIRC, it is
clear that unless authorized by the CIR himself or by his duly authorized representative, through an
LOA, an examination of the taxpayer cannot ordinarily be undertaken. The circumstances
contemplated under Section 6 where the taxpayer may be assessed through best-evidence
obtainable, inventory-taking, or surveillance among others has nothing to do with the LOA. These are
simply methods of examining the taxpayer in order to arrive at the correct amount of taxes. Hence,
unless undertaken by the CIR himself or his duly authorized representatives, other tax agents may
not validly conduct any of these kinds of examinations without prior authority. In this case, there is
no dispute that no LOA was issued prior to the issuance of a PAN and FAN against MEDICARD.
Therefore no LOA was also served on (MEDICARD PHILIPPINES, INC. VS. COMMISSIONER OF
INTERNAL REVENUE, GR NO. 222743, APRIL 5, 2017, REYES, J.)
Page 25 of 53

As stated by the CTA, the BIR cannot shift the blame to the taxpayer for issuing defective waivers.
The Court has ruled that the BIR cannot hide behind the doctrine of estoppel to cover its failure to
comply with RMO 20-90 and RDAO 05-01 which were issued by the BIR itself. A waiver of the statute
of limitations is a derogation of the taxpayer's right to security against prolonged and unscrupulous
investigations and thus, it must be carefully and strictly construed. Since the three Waivers in this
case are defective, they do not produce any effect and did not suspend the three-year prescriptive
period under Section 203 of the NIRC. (CIR VS. PHILIPPINE DAILY INQUIRER, GR NO. 213943,
MARCH 22, 2017, CARPIO, J.)

Tax assessments should first go through appropriate tax proceedings prescribed by law. The present
case is neither the proper venue nor the forum to determine the validity of these alleged pending tax
assessments or to declare its inclusion in the computation of just compensation inasmuch as these
were not presented before the lower courts. (REPUBLIC OF THE PHILIPPINES VS. HON. JESUS
MUPAS, G.R. NO. 181892, APRIL 19, 2016, J. BRION)

A notice of assessment fixes and determines the tax liabilty of a taxpayer and is a notice to the effect
that the amount stated therein is due as tax and a demand to pay thereof. A notice of assessment as
provided for in the Real Property Tax Code should effectively inform the taxpayer of the value of a
specific property, or proportion thereof subject to tax, including the discovery, listing, classification,
and appraisal of properties. Nowhere does the resolution state that the tax declarations can be
considered as notices of assessment. (ROMEO PUCYUTAN, FOR AND IN BEHALF OF THE CITY OF
MUNTINLUPA, METRO MANILA AS ITS TREASURER VS. MANILA ELECTRIC COMPANY, G.R. NO.
197136, APRIL 18, 2016, J. PERALTA)

A "decision" differs from an "assessment" and failure of the FDDA to state the facts and law on which
it is based renders the decision void - but not necessarily the assessment. RR No. 12-99 where it is
stated that failure of the FDDA to reflect the facts and law on which it is based will make the decision
void does not extend to the nullification of the entire assessment. Tax laws may not be extended by
implication beyond the clear import of their language, nor their operation enlarged so as to embrace
matters not specifically provided. (COMMISSIONER OF INTERNAL REVENUE VS. LIQUIGAZ
PHILIPPINES CORPORATION, G.R. NO. 215534 AND G.R. NO. 215557, APRIL 18, 2016, J.
MENDOZA)

Nevertheless, the appraisal and assessment of the transformers, electric posts, transmission lines,
insulators, and electric meters of MERALCO as machinery under Tax Declaration Nos. 019-6500 and
019-7394 were not in accordance with the Local Government Code and in violation of the right to
due process of MERALCO and, therefore, null and void.

It appears that the City Assessor of Lucena simply lumped together all the transformers, electric
posts, transmission lines, insulators, and electric meters of MERALCO located in Lucena City under
Tax Declaration Nos. 019-6500 and 019-7394, contrary to the specificity demanded under Sections
224 and 225 of the Local Government Code for appraisal and assessment of machinery. It is apparent
from these two provisions that every machinery must be individually appraised and assessed
depending on its acquisition cost, remaining economic life, estimated economic life, replacement or
reproduction cost, and depreciation. The City Assessor and the City Treasurer of Lucena did not even
provide the most basic information such as the number of transformers, electric posts, insulators,
Page 26 of 53

and electric meters or the length of the transmission lines appraised and assessed under Tax
Declaration Nos. 019-6500 and 019-7394. There is utter lack of factual basis for the assessment of
the transformers, electric posts, transmission lines, insulators, and electric meters of MERALCO. It is
true that tax assessments by tax examiners are presumed correct and made in good faith, with the
taxpayer having the burden of proving otherwise. In this case, MERALCO was able to overcome the
presumption. (MANILA ELECTRIC COMPANY VS. THE CITY ASSESSOR AND CITY TREASURER OF
LUCENA CITY G.R. NO. 166102. AUGUST 5, 2015)

The notice requirement under Section 228 of the NIRC is substantially complied with whenever the
taxpayer had been fully informed in writing of the factual and legal bases of the deficiency taxes
assessment, which enabled the latter to file an effective protest. (SAMAR-I ELECTRIC
COOPERATIVE VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 193100, DECEMBER 10,
2014, J. VILLARAMA, JR.)

Spouses Manly were charged with tax evasion due to their under declaration of income in their ITR.
The investigation of the revenue officers shows that the under declaration exceeded 30% of the
declared income of the spouses. The Spouses Manly opposed the said complaint due to the lack of
deficiency tax assessment. In this case, the Court ruled that tax evasion is deemed complete when the
violator has knowingly and willfully filed a fraudulent return with intent to evade and defeat a part
or all of the tax. Corollarily, an assessment of the tax deficiency is not required in a criminal
prosecution for tax evasion. However, in Commissioner of Internal Revenue v. Court of Appeals, we
clarified that although a deficiency assessment is not necessary, the fact that a tax is due must first
be proved before one can be prosecuted for tax evasion. (BUREAU OF INTERNAL REVENUE, AS
REPRESENTED BY THE COMMISSIONER OF INTERNAL REVENUE VS. COURT OF APPEALS,
SPOUSES ANTONIO VILLAN MANLY, AND RUBY ONG MANLY, G.R. NO. 197590, NOVEMBER 24,
2014, J. DEL CASTILLO)

PRESCRIPTIVE PERIOD OF ASSESSMENT

Section 203 of the NIRC, the prescriptive period to assess is set at three years. This rule is subject to
the exceptions provided under Section 222 of the NIRC. In Commissioner of Internal Revenue v.
Javier, this Court ruled that fraud is never imputed. The Court stated that it will not sustain findings
of fraud upon circumstances which, at most, create only suspicion. The Court added that the mere
understatement of a tax is not itself proof of fraud for the purpose of tax evasion. Thus, while the
filing of a fraudulent return necessarily implies that the act of the taxpayer was intentional and done
with intent to evade the taxes due, the filing of a false return can be intentional or due to honest
mistake. In CIR v. B.F. Goodrich Phils., Inc., the Court stated that the entry of wrong information due
to mistake, carelessness, or ignorance, without intent to evade tax, does not constitute a false return.
In this case, we do not find enough evidence to prove fraud or intentional falsity on the part of PDI.
Indeed, the Waivers executed by the BIR and PDI were meant to extend the three-year prescriptive
period, and would have extended such period were it not for the defects found by the CTA. This
further shows that at the outset, the BIR did not find any ground that would make the assessment fall
under the exceptions. Clearly, the defects in the Waivers resulted to the non-extension of the period
to assess or collect taxes, and made the assessments issued by the BIR beyond the three-year
prescriptive period void. (CIR VS. PHILIPPINE DAILY INQUIRER, GR NO. 213943, MARCH 22,
2017, CARPIO, J.)

Page 27 of 53

Generally, internal revenue taxes shall be assessed within three (3) years after the last day prescribed
by law for the filing of the return, or where the return is filed beyond the period, from the day the
return was actually filed. Section 222 of the NIRC, however, provides for exceptions to the general
rule. It states that in the case of a false or fraudulent return with intent to evade tax or of failure to
file a return, the assessment may be made within ten (10) years from the discovery of the falsity,
fraud or omission. Thus, a mere showing that the returns filed by the taxpayer were false,
notwithstanding the absence of intent to defraud, is sufficient to warrant the application of the ten
(10) year prescriptive period under Section 222 of the NIRC. Under Section 248(B) of the NIRC, there
is a prima facie evidence of a false return if there is a substantial underdeclaration of taxable sales,
receipt or income. The failure to report sales, receipts or income in an amount exceeding 30% what
is declared in the returns constitute substantial underdeclaration. In other words, when there is a
showing that a taxpayer has substantially underdeclared its sales, receipt or income, there is a
presumption that it has filed a false return. As such, the CIR need not immediately present evidence
to support the falsity of the return, unless the taxpayer fails to overcome the presumption against it.
(COMMISSIONER OF INTERNAL REVENUE VS. ASALUS CORPORATION, G.R. NO. 221590,
FEBRUARY 22, 2017, MENDOZA, J.)

It is true that neither the FAN nor the FDDA explicitly stated that the applicable prescriptive period
was the ten (10)-year period set in Section 222 of the NIRC. They, however, made reference to the
PAN, which categorically stated that "[t]he running of the three-year statute of limitation as provided
under Section 203 of the 1997 National Internal Revenue Code (NIRC) is not applicable xxx but rather
to the ten (10) year prescriptive period pursuant to Section 222(A) of the tax code xxx." In Samar-I
Electric Cooperative v. COMELEC, the Court ruled that it sufficed that the taxpayer was substantially
informed of the legal and factual bases of the assessment enabling him to file an effective protest.
Thus, substantial compliance with the requirement as laid down under Section 228 of the NIRC
suffices, for what is important is that the taxpayer has been sufficiently informed of the factual and
legal bases of the assessment so that it may file an effective protest against the assessment.
(COMMISSIONER OF INTERNAL REVENUE VS. ASALUS CORPORATION, G.R. NO. 221590,
FEBRUARY 22, 2017, MENDOZA, J.)

The CIR has three (3) years from the date of the actual filing of the return or from the last day
prescribed by law for the filing of the return, whichever is later, to assess internal revenue taxes.
Here, GJM filed its Annual Income Tax Return for the taxable year 1999 on April 12, 2000. The three
(3)-year prescriptive period, therefore, was only until April 15, 2003. The records reveal that the BIR
sent the FAN through registered mail on April 14, 2003, well-within the required period. The Court
has held that when an assessment is made within the prescriptive period, as in the case at bar, receipt
by the taxpayer may or may not be within said period. But it must be clarified that the rule does not
dispense with the requirement that the taxpayer should actually receive the assessment notice, even
beyond the prescriptive period. GJM, however, denies ever having received any FAN. If the taxpayer
denies having received an assessment from the BIR, it then becomes incumbent upon the latter to
prove by competent evidence that such notice was indeed received by the addressee. Here, the onus
probandi has shifted to the BIR to show by contrary evidence that GJM indeed received the
assessment in the due course of mail. It has been settled that while a mailed letter is deemed received
by the addressee in the course of mail, this is merely a disputable presumption subject to
controversion, the direct denial of which shifts the burden to the sender to prove that the mailed
letter was, in fact, received by the addressee. (COMMISSIONER OF INTERNAL REVENUE VS. GJM
PHILIPPINES MANUFACTURING, INC., GR. NO. 202695, FEBRUARY 29, 2016, J. PERALTA)
Page 28 of 53

The Court has held that when an assessment is made within the prescriptive period, as in the case at
bar, receipt by the taxpayer may or may not be within said period. But it must be clarified that the
rule does not dispense with the requirement that the taxpayer should actually receive the assessment
notice, even beyond the prescriptive period. If the taxpayer denies having received an assessment
from the BIR, it then becomes incumbent upon the latter to prove by competent evidence that such
notice was indeed received by the addressee. Here, the onus probandi has shifted to the BIR to show
by contrary evidence that GJM indeed received the assessment in the clue course of mail. It has been
settled that while a mailed letter is deemed received by the addressee in the course of mail, this is
merely a disputable presumption subject to controversion, the direct denial of which shifts the
burden to the sender to prove that the mailed letter was, in fact, received by the addressee. To prove
the fact of mailing, it is essential to present the registry receipt issued by the Bureau of Posts or the
Registry return card which would have been signed by the taxpayer or its authorized representative.
(COMMISSIONER OF INTERNAL REVENUE VS. GJM PHILIPPINES MANUFACTURING, INC., G.R.
NO. 202695. FEBRUARY 29, 2016)

The general rule is that when a waiver does not comply with the requisites for its validity specified
under RMO No. 20-90 and RDAO 01-05, it is invalid and ineffective to extend the prescriptive period
to assess taxes. However, due to its peculiar circumstances, we shall treat this case as an exception
to this rule and find the Waivers valid for the reasons discussed below. First, the parties in this case
are in pari delicto or in equal fault. As between the parties, it would be more equitable if
petitioners lapses were allowed to pass and consequently uphold the Waivers in order to support
this principle and public policy. Second, the Court has repeatedly pronounced that parties must come
to court with clean hands. Following the foregoing principle, respondent should not be allowed to
benefit from the flaws in its own Waivers and successfully insist on their invalidity in order to evade
its responsibility to pay taxes. Finally, the Court cannot tolerate this highly suspicious situation. In
this case, the taxpayer, on the one hand, after voluntarily executing waivers, insisted on their
invalidity by raising the very same defects it caused. (COMMISSIONER OF INTERNAL REVENUE VS.
NEXT MOBILE, INC., G.R. NO. 212825. DECEMBER 7, 2015)

A waiver is not automatically a renunciation of the right to invoke the defense of prescription. A
waiver of the Statute of Limitations is nothing more than an agreement between the taxpayer and
the Bureau of Internal Revenue (BIR) that the period to issue an assessment and collect the taxes due
is extended to a date certain. It is a bilateral agreement, thus necessitating the very signatures of
both the CIR and the taxpayer to give birth to a valid agreement. Furthermore, indicating in the
waiver the date of acceptance by the BIR is necessary in order to determine whether the parties (the
taxpayer and the government) had entered into a waiver before the expiration of the time
prescribed in Section 203 (the three-year prescriptive period) for the assessment of the tax. When
the period of prescription has expired, there will be no more need to execute a waiver as there will
be nothing more to extend. Hence, no implied consent can be presumed, nor can it be contended that
the concurrence to such waiver is a mere formality. (COMMISSIONER OF INTERNAL REVENUE VS.
STANDARD CHARTERED BANK, G.R. NO. 192173. JULY 29, 2015)

The assessment of the tax is deemed made and the three-year period for collection of the assessed
tax begins to run on the date the assessment notice had been released, mailed or sent by the BIR to
the taxpayer. Thus, failure of the BIR to file a warrant of distraint or serve a levy on taxpayer's
properties nor file collection case within the three-year period is fatal. Also, the attempt of the BIR to
Page 29 of 53

collect the tax through its Answer with a demand for the taxpayer to pay the assessed DST in the
CTA is not deemed compliance with the Tax Code. (CHINA BANKING CORPORATION VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 172509, FEBRUARY 04, 2015, C.J. SERENO)

Section 203 of the NIRC sets the three-year prescriptive period to assess. However the exceptions are
provided under Section 222 of the NIRC of 1997. In the case at bar, it was petitioners substantial
under declaration of withholding taxes in the amount of P2,690,850.91 which constituted the falsity
in the subject returns giving respondent the benefit of the period under Section 222 of the NIRC of
1997 to assess the correct amount of tax at any time within ten (10) years after the discovery of the
falsity, fraud or omission. (SAMAR-I ELECTRIC COOPERATIVE VS. COMMISSIONER OF INTERNAL
REVENUE, G.R. NO. 193100. DECEMBER 10, 2014, J. VILLARAMA JR.)

It is clear that the assailed deficiency tax assessment for the EWT in 1994 disregarded the provisions
of Section 228 of the [NIRC], as amended, as well as Section 3.1.4 of the Revenue Regulations No. 12-
99 by not providing the legal and factual bases of the assessment. Hence, the formal letter of demand
and the notice of assessment issued relative thereto are void. The statute of limitations on assessment
and collection of national internal taxes was shortened from five (5) years to three (3) years by virtue
of Batas Pambansa Blg. 700. Thus, [Petitioner CIR] has three (3) years from the date of actual filing
of the tax return to assess a national internal revenue tax or to commence court proceedings for the
collection thereof without an assessment. However, when it validly issues an assessment within the
three (3) year period, it has another three (3) years within which to collect the tax due by distraint,
levy, or court proceeding. (COMMISSIONER OF INTERNAL REVENUE VS. UNITED SALVAGE AND
TOWAGE (PHILS.), INC., G.R. NO. 197515, JULY 2, 2014, J. PERALTA)

ASSESSMENT PROCESS

In this case the issue was whether or not the Trust Indenture Agreements entered into by Traders
Royal Bank and its clients constituted deposits or trusts. If it was a deposit then it will be subject to
documentary stamp tax. The Supreme Court held that the only way to determine the relationship
between the parties is to examine the terms and conditions provided under the actual indenture
agreement. However TRB failed to produce the actual agreement. In contrast, the BIR examiners
conducted a thorough audit and investigation of the books of account of TRB. The audit and
investigation resulted in the issuance of Assessment Notices against TRB for DST tax liabilities for
1996 and 1997, which were duly received by TRB. The tax assessments by tax examiners are
presumed correct and made in good faith. The taxpayer has the duty to prove otherwise. Therefore
the agreements were considered as deposits subject to DST. (COMMISSIONER OF INTERNAL
REVENUE VS, TRADERS ROYAL BANK, G.R. NO. 167134. MARCH 18, 2015, J. LEONARDO-DE
CASTRO)

Petitioner questions the decision of the CTA holding that its right to assess respondent of its tax
deficiencies for the taxable year 1999 has already prescribed for its failure to send the Formal
Assessment Notice to respondents new address despite respondents failure to give petitioner a
formal written notice of its change of address. The SC ruled that despite the absence of a formal
written notice of respondent's change of address, the fact remains that petitioner became aware of
respondent's new address as shown by the documents replete in its records. As a consequence, the
running of the three-year period to assess respondent was not suspended and has already
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prescribed. (COMMISSIONER OF INTERNAL REVENUE VS. BASF COATING + INKS PHILS., INC.,
G.R. NO. 198677, NOVEMBER 26, 2014, J. PERALTA)

COMMISSIONERS ACTION EQUIVALENT TO DENIAL OF PROTEST

Under Section 112(C) of the NIRC, in case of failure on the part of the CIR to act on the application,
the taxpayer affected may, within 30 days after the expiration of the 120-day period, appeal the
unacted claim with the CTA. If the Commissioner fails to decide within a specific period required
by law, such inaction shall be deemed a denial of the application for tax refund or credit. In this
case, when TSC filed its administrative claim on 21 December 2005, the CIR had a period of 120 days,
or until 20 April 2006, to act on the claim. However, the CIR failed to act on TSCs claim within this
120-day period. Thus, TSC filed its petition for review with the CTA on 24 April 2006 or within 30
days after the expiration of the 120-day period. Hence, the judicial claim was not prematurely filed.
(COMMISSIONER OF INTERNAL REVENUE VS. TEAM SUAL CORPORATION, G.R. NO. 205055,
JULY 18, 2014, J. CARPIO)

COLLECTION

SUSPENSION OF COLLECTION OF TAXES

The CTA may order the suspension of the collection of taxes provided that the taxpayer either: (1)
deposits the amount claimed; or (2) files a surety bond for not more than double the amount. The
surety bond amounting to P4,467,391,881.76 imposed by the CTA was within the parameters
delineated in Section 11 of R.A. 1125, as amended. The Court holds, however, that the CTA in Division
gravely abused its discretion under Section 11 because it fixed the amount of the bond at nearly five
times the net worth of the petitioner without conducting a preliminary hearing to ascertain whether
there were grounds to suspend the collection of the deficiency assessment on the ground that such
collection would jeopardize the interests of the taxpayer. Moreover, Section 11 of R.A. 1125, as
amended, indicates that the requirement of the bond as a condition precedent to suspension of the
collection applies only in cases where the processes by which the collection sought to be made by
means thereof are carried out in consonance with the law, not when the processes are in plain
violation of the law that they have to be suspended for jeopardizing the interests of the taxpayer.
(TRIDHARMA MARKETING CORPORATION vs. COURT OF TAX APPEALS, SECOND DIVISION,
AND THE COMMISSIONER OF INTERNAL REVENUE, G.R. No. 215950, June 20, 2016, J.
BERSAMIN)

PRESCRIPTIVE PERIOD

There is a distinction between a request for reconsideration and a request for reinvestigation. A
reinvestigation which entails the reception and evaluation of additional evidence will take more time
than a reconsideration of a tax assessment, which will be limited to the evidence already at hand; this
justifies why the reinvestigation can suspend the running of the statute of limitations on collection of
the assessed tax, while the reconsideration cannot. Hence, the period for BIR to collect the deficiency
DST already prescribed as the protest letter of BPI was a request for reconsideration, which did not
suspend the running of the prescriptive period to collect. (BANK OF THE PHILIPPINE ISLANDS VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 181836, JULY 9, 2014, J. CARPIO)

Page 31 of 53

TAX EXEMPTIONS

We take judicial notice that on 25 July 2016, the present CIR Caesar R. Dulay issued RMO No. 44-
2016. It is clear and unmistakable from the aforequoted constitutional provision that non-stock, non-
profit educational institutions are constitutionally exempt from tax on all revenues derived in
pursuance of its purpose as an educational institution and used actually, directly and exclusively for
educational purposes. This constitutional exemption gives the non-stock, non-profit educational
institutions a distinct character. And for the constitutional exemption to be enjoyed, jurisprudence
and tax rulings affirm the doctrinal rule that there are only two requisites:
(1) The school must be non-stock and non-profit; and
(2) The income is actually, directly and exclusively used for educational purposes.
There are no other conditions and limitations. In this light, the constitutional conferral of tax
exemption upon non-stock and non-profit educational institutions should not be implemented or
interpreted in such a manner that will defeat or diminish the intent and language of the Constitution.
(HON. KIM S. JACINTO-HENARES VS. ST. PAUL COLLEGE OF MAKATI, G.R. NO. 215383, MARCH
8, 2017, CARPIO, J.)

Section 13 of PD No. 1869 evidently states that payment of the 5% franchise tax by PAGCOR and its
contractees and licensees exempts them from payment of any other taxes, including corporate
income tax. This provision providing for the said exemption was neither amended nor repealed by
any subsequent laws (i.e. Section 1 of R.A. No. 9337 which amended Section 27(C) of the NIRC of
1997); thus, it is still in effect. Guided by the doctrinal teachings in resolving the case at bench, it is
without a doubt that, like PAGCOR, its contractees and licensees remain exempted from the payment
of corporate income tax and other taxes since the law is clear that said exemption inures to their
benefit. As the PAGCOR Charter states in unequivocal terms that exemptions granted for earnings
derived from the operations conducted under the franchise specifically from the payment of any tax,
income or otherwise, as well as any form of charges, fees or levies, shall inure to the benefit of and
extend to corporation(s), association(s), agency(ies), or individual(s) with whom the PAGCOR or
operator has any contractual relationship in connection with the operations of the casino(s)
authorized to be conducted under this Franchise, so it must be that all contractees and licensees of
PAGCOR, upon payment of the 5% franchise tax, shall likewise be exempted from all other taxes,
including corporate income tax realized from the operation of casinos. Plainly, too, upon payment of
the 5% franchise tax, petitioner's income from its gaming operations of gambling casinos, gaming
clubs and other similar recreation or amusement places, and gaming pools, defined within the
purview of the aforesaid section, is not subject to corporate income tax. (BLOOMBERRY RESORTS
AND HOTELS, INC, v. BUREAU OF INTERNAL REVENUE, REPRESENTED BY COMMISSIONER KIM
S. JACINTO-HENARES, G.R. No. 212530, August 10, 2016, J. PEREZ)

TAX REFUND/CREDIT

We have consistently ruled that claims for tax refunds, when based on statutes granting tax
exemption, partake of the nature of an exemption. Tax refunds and exemptions are exceptions rather
than the rule and for this reason are highly disfavored. Hence, in evaluating a claim for refund, the
rule of strict interpretation applies. This rule requires the claimant to prove not only his entitlement
to refund, but also his due observance of the reglementary periods within which he must file his
administrative and judicial claims for refund. Non-compliance with these substantive and procedural
Page 32 of 53

due process requirements results in the denial of the claim. (COMMISSIONER OF INTERNAL
REVENUE VS. UNITED CADIZ SUGAR FARMERS ASSOCIATION MULTI-PURPOSE COOPERATIVE,
G.R. NO. 209776, DECEMBER 7, 2016, J. BRION)

We therefore hold that respondent, as the statutory taxpayer who is directly liable to pay the excise
tax on its petroleum products, is entitled to a refund or credit of the excise taxes it paid for petroleum
products sold to international carriers, the latter having been granted exemption from the payment
of said excise tax under Sec.135(a) of the NIRC. (COMMISSIONER OF INTERNAL REVENUE VS.
PILIPINAS SHELL PETROLEUM CORPORATION, G.R. NO. 180402. FEBRUARY 10, 2016)

Pursuant to Section 112 of the National Internal Revenue Code (NIRC) of 1997 the requisites for
claiming unutilized/excess input VAT, except transitional input VAT, are as follows: 1)The taxpayer-
claimant is VAT registered; 2)The taxpayer-claimant is engaged in zero-rated or effectively zero-
rated sales; 3)There are creditable input taxes due or paid attributable to the zero-rated or effectively
zero-rated sales; 4)This input tax has not been applied against the output tax; and 5)The application
and the claim for a refund have been filed within the prescribed period. (COMMISSIONER OF
INTERNAL REVENUE VS. TOLEDO POWER COMPANY G.R. NOS. 195175 & 199645. AUGUST 10,
2015)

In both C.T.A. Case Nos. 7233 and 7294, the administrative claim for the refund of unutilized input
VAT attributable to the zero-rated or effectively zero-rated sales was timely filed on 23 December
2004, which was within two years from the close of the first and the second quarters of 2003 when
the sales were made. Similarly, this case also falls within the exception period by virtue of BIR Ruling
No. DA-489-03 as recognized in San Roque. In C.T.A. Case No. 7233, TPC filed its judicial claim on 22
April 2005. In theory, the CTA does not have jurisdiction over the Petition, since it was filed on the
last day of the 120-day period for the CIR, or without waiting for the expiration of the aforesaid
period. However, BIR Ruling No. DA-489-03 allows this premature filing. TPC may claim the benefits
of that ruling in its Petition in C.T.A. Case No. 7233 for the refund of the unutilized input VAT
attributable to zero-rated or effectively zero-rated sales for the first quarter of 2003.
(COMMISSIONER OF INTERNAL REVENUE VS. TOLEDO POWER COMPANY G.R. NOS. 195175 &
199645. AUGUST 10, 2015)
The burden of proving entitlement to a tax refund is on the taxpayer. It is logical to assume that in
order to discharge this burden, the law intends the filing of an application for a refund to necessarily
include the filing of complete supporting documents to prove entitlement for the refund. Otherwise,
the mere filing of an application without any supporting document would be as good as filing a mere
scrap of paper. Besides, the taxpayer was already given two (2) years to determine its refundable
taxes and complete the documents necessary to prove its claim. The alleged completion of supporting
documents after the filing of an application for an administrative claim and worse, after the filing
of a judicial claim is tantamount to legal maneuvering. (HEDCOR, INC. VS. COMMISSIONER OF
INTERNAL REVENUE, G.R. NO. 207575. JULY 15, 2015)

For a claim for refund to be granted, the manner in proving it must be in accordance with the
prescribed rules of evidence. It would have been erroneous had the CTA En Banc relied on
petitioner's own Excise Tax Refund Computation Summary or the unsatisfactory explanation of its
lone witness to justify its claim for tax refund. As it has been said, time and again, that claims for tax
refunds are in the nature of tax exemptions which result in loss of revenue for the government. Upon
the person claiming an exemption from tax payments rests the burden of justifying the exemption by
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words too plain to be mistaken and too categorical to be misinterpreted; it is never presumed nor be
allowed solely on the ground of equity. In addition, one who claims that he is entitled to a tax refund
must not only claim that the transaction subject of tax is clearly and unequivocally not subject to tax
-the amount of the claim must still be proven in the normal course, in accordance with the prescribed
rules on evidence. (FORTUNE TOBACCO CORPORATION VS. COMMISSIONER OF INTERNAL
REVENUE, G.R. NO. 192024. JULY 1, 2015)

Those who claim for refund must not only prove its entitlement to the excess credits, but likewise
must prove that no carry-over has been made in cases where refund is sought. However, proving that
no carry-over has been made does not absolutely require the presentation of the quarterly ITRs. With
Winebrenner & Inigo Insurance Brokers, Inc. having complied with the requirements for refund, and
without the CIR showing contrary evidence other than its bare assertion of the absence of the
quarterly ITRs, copies of which are easily verifiable by its very own records, the burden of proof of
establishing the propriety of the claim for refund has been sufficiently discharged. Hence, the grant
of refund is proper. (WINEBRENNER & IIGO INSURANCE BROKERS, INC. VS. COMMISSIONER OF
INTERNAL REVENUE, G.R. NO. 206526, JANUARY 28, 2015, J. MENDOZA)

The requirements for entitlement of a corporate taxpayer for a refund or the issuance of tax credit
certificate involving excess withholding taxes are as follows: 1) That the claim for refund was filed
within the two-year reglementary period pursuant to Sec. 229 of the NIRC; 2) When it is shown on
the ITR that the income payment received is being declared part of the taxpayers gross income; and
3) When the fact of withholding is established by a copy of the withholding tax statement, duly issued
by the payor to the payee, showing the amount paid and income tax withheld from that amount.
Relevant to the instant case is requirements numbers 2 and 3, which were duly proved by TPEC, as
found by the courts a quo. With regard to the second requirement, it is fundamental that the findings
of fact by the CTA in Division are not to be disturbed without any showing of grave abuse of discretion
considering that the members of the Division are in the best position to analyze the documents
presented by the parties. Consequently, the Court adopts the findings of the CTA in Division, which
the CTA En Banc concurred with. (REPUBLIC OF THE PHILIPPINES, REPRESENTED BY THE
COMMISSIONER OF INTERNAL REVENUE VS. TEAM (PHILS.) ENERGY CORPORATION
(FORMERLY MIRANT PHILS ENERGY CORPORATION), G.R. NO. 188016, JANUARY 14, 2015, J.
BERSAMIN)

In this case, Duty Free Philippines claimed that it was exempted from the expanded withholding tax
under Revenue Regulation (R.R.) No. 6-94. The CTA Division ruled that Duty Free was not a tax-
exempt entity in the absence of an express grant of tax exemption. Duty Free then directly appealed
to the Supreme Court under Rule 45. The Supreme Court said that Duty Frees direct appeal to this
Court is fatal to its claim. Under RA 9282 Section 18, A party adversely affected by a resolution of a
Division of the CTA on a motion for reconsideration or new trial, may file a petition for review with
the CTA en banc. Clearly, the Supreme Court is without jurisdiction to review decisions rendered by
a division of the CTA, exclusive appellate jurisdiction over which is vested in the CTA en banc. (DUTY
FREE PHILIPPINES VS. BUREAU OF INTERNAL REVENUE, REPRESENTED BY HON. ANSELMO G.
ADRIANO, ACTING REGIONAL DIRECTOR, REVENUE REGION NO. 8, MAKATI CITY, G.R NO.
197228, OCTOBER 8, 2014. SERENO.)

The certificate of creditable tax withheld at source is the competent proof to establish the fact that
taxes are withheld. It is not necessary for the person who executed and prepared the certificate of
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creditable tax withheld at source to be presented and to testify personally to prove the authenticity
of the certificates. In Banco Filipino Savings and Mortgage Bank v. Court of Appeals, this court
declared that a certificate is complete in the relevant details that would aid the courts in the
evaluation of any claim for refund of excess creditable withholding taxes. In fine, the document which
may be accepted as evidence of the third condition, that is, the fact of withholding, must emanate
from the payor itself, and not merely from the payee, and must indicate the name of the payor, the
income payment basis of the tax withheld, the amount of the tax withheld and the nature of the tax
paid. (COMMISSIONER OF INTERNAL REVENUE VS. PHILIPPINE NATIONAL BANK, G.R. NO.
180290 SEPTEMBER 29, 2014, J. LEONEN)

Tax refunds are based on the general premise that taxes have either been erroneously or excessively
paid. Though the Tax Code recognizes the right of taxpayers to request the return of such
excess/erroneous payments from the government, they must do so within a prescribed period.
Further, "a taxpayer must prove not only his entitlement to a refund, but also his compliance with
the procedural due process as non-observance of the prescriptive periods within which to file the
administrative and the judicial claims would result in the denial of his claim." In the case at bar,
MERALCO had ample opportunity to verify on the tax-exempt status of NORD/LB for purposes of
claiming tax refund. Nevertheless, it only filed its claim for tax refund ten (10) months from the
issuance of the aforesaid Ruling. (COMMISSIONER OF INTERNAL REVENUE VS. MANILA ELECTRIC
COMPANY (MERALCO), G.R. NO. 181459, JUNE 9, 2014, J. PERALTA)

Under the first option, any tax on income that is paid in excess of the amount due the government
may be refunded, provided that a taxpayer properly applies for the refund. On the other hand, the
second option works by applying the refundable amount against the tax liabilities of the petitioner in
the succeeding taxable years. Hence, instead of moving for the issuance of a writ of execution relative
to the aforesaid decision, petitioner should have merely requested for the approval of the City of
Manila in implementing the tax refund or tax credit, whichever is appropriate. In other words, no
writ was necessary to cause the execution thereof, since the implementation of the tax refund will
effectively be a return of funds by the City of Manila in favor of petitioner while a tax credit will merely
serve as a deduction of petitioners tax liabilities in the future. Accordingly, while we find merit in
petitioners contention that there are two (2) ways by which respondents may satisfy the judgment
of the RTC-Manila: (1) to pay the petitioner the amount of Php3,036,887.33 as tax refund; or (2) to
issue a tax credit certificate in the same amount which may be credited by petitioner from its future
tax liabilities due to the respondent City of Manila, the issuance of the Writ of Execution relative
thereto was superfluous, because the judgment of the RTC-Manila can neither be considered a
judgment for a specific sum of money susceptible of execution by levy or garnishment under Section
9,Rule 39 of the Rules of Court nor a special judgment under Section 11, Rule 39 thereof. (COCA-
COLA BOTTLERS PHILIPPINES, INC. VS. CITY OF MANILA, ET AL., G.R. NO. 197561, APRIL 7,
2014, J. PERALTA)

There are three essential conditions for the grant of a claim for refund of creditable withholding
income tax, to wit: (1) the claim is filed with the Commissioner of Internal Revenue within the two-
year period from the date of payment of the tax (2) it is shown on the return of the recipient that the
income payment received was declared as part of the gross income and (3) the fact of withholding
is established by a copy of a statement duly issued by the payor to the payee showing the amount
paid and the amount of the tax withheld therefrom. (COMMISSIONER OF INTERNAL REVENUE VS.
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TEAM [PHILIPPINES] OPERATIONS CORPORATION [FORMERLY MIRANT (PHILS)
OPERATIONS CORPORATION], G.R. NO. 179260, APRIL 2, 2014, J. PEREZ)

In Banco Filipino Savings and Mortgage Bank v. Court of Appeals, the Supreme Court laid down the
three essential conditions for the grant of a claim for refund of creditable withholding income tax,
namely: (1) the claim is filed with the Commissioner of Internal Revenue within the two-year period
from the date of payment of the tax; (2) it is shown on the return of the recipient that the income
payment received was declared as part of the gross income; and (3) the fact of withholding is
established by a copy of a statement duly issued by the payor to the payee showing the amount paid
and the amount of the tax withheld therefrom. (COMMISSIONER OF INTERNAL REVENUE, VS.
TEAM [PHILIPPINES] OPERATIONS CORPORATION [FORMERLY MIRANT (PHILS) OPERATIONS
CORPORATION], G.R. NO. 179260, APRIL 2, 2014, J. PEREZ)

Neither the law nor the implementing rules state that a court ruling that has not attained finality
would preclude the availment of the benefits of the Tax Amnesty Law. While tax amnesty, similar to
a tax exemption, must be construed strictly against the taxpayer and liberally in favor of the taxing
authority, it is also a well-settled doctrine that the rule-making power of administrative agencies
cannot be extended to amend or expand statutory requirements or to embrace matters not originally
encompassed by the law. Administrative regulations should always be in accord with the provisions
of the statute they seek to carry into effect, and any resulting inconsistency shall be resolved in favor
of the basic law. (CS GARMENT, INC., VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO.
182399, MARCH 12, 2014, CJ. SERENO)

A tax credit or refund is strictly construed against the taxpayer. Strict compliance with the mandatory
and jurisdictional conditions prescribed by law to claim such tax refund or credit is essential and
necessary for such claim to prosper. Noncompliance with the mandatory periods, nonobservance of
the prescriptive periods, and nonadherence to exhaustion of administrative remedies bar a
taxpayers claim for tax refund or credit, whether or not the CIR questions the numerical correctness
of the claim of the taxpayer. (SILICON PHILIPPINES, INC., (FORMERLY INTEL PHILIPPINES
MANUFACTURING INC.), VS. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 184360 &
184361/COMMISSIONER OF INTERNAL REVENUE VS. SILICON PHILIPPINES, INC., (FORMERLY
INTEL PHILIPPINES MANUFACTURING, INC.) G.R. NO. 184384, FEBRUARY 19, 2014, J.
VILLARAMA, JR.)
Pilipinas Shell, as the statutory taxpayer who is directly liable to pay the excise tax on its petroleum
products, is entitled to a refund or credit of the excise taxes it paid for petroleum products sold to
international carriers, the latter having been granted exemption from the payment of said excise tax
under Sec. 135 (a) of the NIRC. (COMMISSIONER OF INTERNAL REVENUE VS. PILIPINAS SHELL
PETROLEUM CORPORATION, G.R. NO. 188497, FEBRUARY 19, 2014, J. VILLARAMA JR.)

STATUTORY BASIS FOR TAX REFUND UNDER THE TAX CODE

Prescriptive Period for Recovery of Tax

Section 204 of the National Internal Revenue Code, as amended, provides the CIR with, inter alia, the
authority to grant tax refunds. In this relation, Section 229 of the same Code provides for the proper
procedure in order to claim for such refunds. As may be gleaned from the foregoing provisions, a
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claimant for refund must first file an administrative claim for refund before the CIR, prior to filing a
judicial claim before the CTA. Notably, both the administrative and judicial claims for refund should
be filed within the two (2)-year prescriptive period indicated therein, and that the claimant is allowed
to file the latter even without waiting for the resolution of the former in order to prevent the
forfeiture of its claim through prescription. In this regard, case law states that "the primary purpose
of filing an administrative claim [is] to serve as a notice of warning to the CIR that court action would
follow unless the tax or penalty alleged to have been collected erroneously or illegally is refunded.
To clarify, Section 229 of the Tax Code -then Section 306 of the old Tax Code -however does not mean
that the taxpayer must await the final resolution of its administrative claim for refund, since doing so
would be tantamount to the taxpayer's forfeiture of its right to seek judicial recourse should the two
(2)-year prescriptive period expire without the appropriate judicial claim being filed."
(METROBANK AND TRUST COMPANY vs. THE COMMISSIONER OF INTERNAL REVENUE, G.R. No.
182582, APRIL 17, 2017, PERLAS-BERNABE, J.)

UCSFA-MPC's claim for refund -grounded as it is on payments of advance VAT alleged to have been
illegally and erroneously collected from November 15, 2007 to February 13, 2009 -is governed by
Sections 204(C) and 229 of the NIRC. These provisions are clear: within two years from the date of
payment of tax, the claimant must first file an administrative claim with the CIR before filing its
judicial claim with the courts of law. Both claims must be filed within a two-year reglementary period.
Timeliness of the filing of the claim is mandatory and jurisdictional. The court cannot take cognizance
of a judicial claim for refund filed either prematurely or out of time. In the present case, the court a
quo found that while the judicial claim was filed merely five days after filing the administrative claim,
both claims were filed within the two-year reglementary period. Thus, the CTA correctly exercised
jurisdiction over the judicial claim filed by UCSFA-MPC. (COMMISSIONER OF INTERNAL REVENUE
vs. UNITED CADIZ SUGAR FARMERS ASSOCIATION MULTI-PURPOSE COOPERATIVE, G.R. NO.
209776, DECEMBER 7, 2016, J. BRION)

Section 229 of the Tax Code states that judicial claims for refund must be filed within two (2) years
from the date of payment of the tax or penalty, providing further that the same may not be maintained
until a claim for refund or credit has been duly filed with the Commissioner of Internal Revenue (CIR).
The primary purpose of filing an administrative claim was to serve as a notice of warning to the CIR
that court action would follow unless the tax or penalty alleged to have been collected erroneously
or illegally is refunded. To clarify, Section 229 of the Tax Code [then Section 306 of the old Tax Code]
however does not mean that the taxpayer must await the final resolution of its administrative claim
for refund, since doing so would be tantamount to the taxpayer's forfeiture of its right to seek judicial
recourse should the two (2)-year prescriptive period expire without the appropriate judicial claim
being filed. (COMMISSIONER OF INTERNAL REVENUE v. GOODYEAR PHILIPPINES, INC., G.R. No.
216130, AUGUST 03, 2016, J. PERLAS-BERNABE)

The administrative claim of a VAT-registered person for the issuance by CIR of tax credit certificates
or the refund of input taxes paid on zero-rated sales or capital goods imported may be made within
two years after the close of the taxable quarter when the sale or importation/purchase was made.
Upon the filing of an administrative claim, respondent is given a period of 120 days within which to
(1) grant a refund or issue the tax credit certificate for creditable input taxes; or (2) make a full or
partial denial of the claim for a tax refund or tax credit. Failure on the part of respondent to act on
the application within the 120-day period shall be deemed a denial. The judicial claim shall be filed
within a period of 30 days after the receipt of respondent's decision or ruling or after the expiration
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of the 120-day period, whichever is sooner. Aside from a specific exception to the mandatory and
jurisdictional nature of the periods provided by the law, any claim filed in a period less than or
beyond the 120+30 days provided by the NIRC is outside the jurisdiction of the CTA. (SILICON
PHILIPPINES, INC. (FORMERLY INTEL PHILIPPINES MANUFACTURING, INC.) VS.
COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 182737, MARCH 02, 2016, CJ SERENO)

Upon the filing of an administrative claim, respondent is given a period of 120 days within which to
(1) grant a refund or issue the tax credit certificate for creditable input taxes; or (2) make a full or
partial denial of the claim for a tax refund or tax credit. Failure on the part of respondent to act on
the application within the 120-day period shall be deemed a denial. Note that the 120-day period
begins to run from the date of submission of complete documents supporting the administrative
claim. If there is no evidence showing that the taxpayer was required to submit -or actually submitted
-additional documents after the filing of the administrative claim, it is presumed that the complete
documents accompanied the claim when it was filed. Whether respondent rules in favor of or against
the taxpayer -or does not act at all on the administrative claim -within the period of 120 days from
the submission of complete documents, the taxpayer may resort to a judicial claim before the CTA.
(SILICON PHILIPPINES, INC. vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 182737.
MARCH 2, 2016)

With the 30-day period always available to the taxpayer, the taxpayer can no longer file a judicial
claim for refund or credit of input VAT without waiting for the Commissioner to decide until the
expiration of the 120-day period. Clearly, MPC's failure to observe the mandatory 120-day period
under the law was fatal to its immediate filing of a judicial claim before the CTA. It rendered the filing
of the CTA petition premature, and barred the tax court from acquiring jurisdiction over the same.
Thus, the dismissal of the petition is in order. (COMMISSIONER OF INTERNAL REVENUE vs.
MIRANT PAGBILAO CORPORATION, G.R. No. 180434. JANUARY 20, 2016)

The rule is that from the date an administrative claim for excess unutilized VAT is filed, a taxpayer
has thirty (30) days within which to submit the documentary requirements sufficient to support
his claim, unless given further extension by the CIR. Then, upon filing by the taxpayer of his complete
documents to support his application, or expiration of the period given, the CIR has 120 days within
which to decide the claim for tax credit or refund. Should the taxpayer, on the date of his filing,
manifest that he no longer wishes to submit any other addition documents to complete his
administrative claim, the 120 day period allowed to the CIR begins to run from the date of filing.
(PILIPINAS TOTAL GAS, INC. vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 207112.
DECEMBER 8, 2015)

Pursuant to Section 112 (A)(4) 2 and (D)(4)3 of the NIRC, a taxpayer has two (2) years from the close
of the taxable quarter when the zero-rated sales were made within which to file with the CIR an
administrative claim for refund or credit of unutilized input VAT attributable to such sales. The CIR,
on the other hand, has 120 days from receipt of the complete documents within which to act on the
administrative claim. Upon receipt of the decision, a taxpayer has 30 days within which to appeal the
decision to the CTA. However, if the 120-day period expires without any decision from the CIR, the
taxpayer may appeal the inaction to the CTA within 30 days from the expiration of the 120-day
period. (COMMISSIONER OF INTERNAL REVENUE vs. TOLEDO POWER COMPANY, G.R. No.
196415. DECEMBER 2, 2015)

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The Court has observed that based on the records, Nippon's administrative claim for the first taxable
quarter of 2002 which closed on March 31, 2002 was already time-barred for being filed on April 22,
2004, or beyond the two (2)-year prescriptive period pursuant to Section 112(A) of the National
Internal Revenue Code of 1997. Although prescription was not raised as an issue, it is well-settled
that if the pleadings or the evidence on record show that the claim is barred by prescription, the Court
may motu proprio order its dismissal on said ground. (COMMISSIONER OF INTERNAL REVENUE vs.
NIPPON EXPRESS (PHILS.) CORPORATION, G.R. No. 212920. SEPTEMBER 16, 2015)

The records show that CE Luzons administrative and judicial claims were filed on November 30,
2006 and January 3, 2007, respectively, or during the period of effectivity of BIR Ruling No. DA-489-
03 and, thus, fell within the window period stated in San Roque, i.e., when taxpayer-claimants need
not wait for the expiration of the 120-day period before seeking judicial relief. Verily, the CTA En
Banc erred when it outrightly dismissed CE Luzons petition on the ground of prematurity. (CE
LUZON GEOTHERMAL POWER COMPANY, INC. vs. COMMISSIONER OF INTERNAL REVENUE,
G.R. No. 200841-42. AUGUST 26, 2015)

In this case, since the filing of the administrative claim was done within the period where BIR Ruling
No. DA-489-03 was recognized valid, TPC is not compelled to observe the 120-day waiting period.
Nevertheless, it should have filed the Petition within 30 days after the expiration of the 120-day
period. San Roque recognized BIR Ruling No. DA-489-03 which allowed the premature filing of a
judicial claim as an exception to the mandatory observance of the 120-day period. By virtue of the
doctrines laid down in San Roque, TPC should have filed its judicial claim from 23 December 2004
until 22 May 2005; however, it filed its Petition to the CTA only on 24 April 2006. TPC lost its right to
claim a refund or credit of its alleged excess input VAT attributable to zero-rated or effectively zero-
rated sales for taxable year 2004 by virtue of its own failure to observe the prescriptive periods.
(COMMISSIONER OF INTERNAL REVENUE vs. TOLEDO POWER COMPANY, G.R. Nos. 195175 &
199645. AUGUST 10, 2015)

Pursuant to Section 112(C) of the NIRC, respondent had 120 days from the date of submission of
complete documents in support of the application within which to decide on the administrative claim.
Thereafter, the taxpayer affected by the CIRs decision or inaction may appeal to the CTA within 30
days from the receipt of the decision or from the expiration of the 120-day period. Compliance
with both periods is jurisdictional, considering that the 30-day period to appeal to the CTA is
dependent on the 120-day period. The period of 120 days is a prerequisite for the commencement of
the 30-day period to appeal. Strict compliance with the 120+30 day period is necessary for a claim
for a refund or credit of input VAT to prosper. An exception to that mandatory period was, however,
recognized in San Roque during the period between 10 December 2003, when BIR Ruling No. DA-
489-03 was issued, and 6 October 2010, when the Court promulgated Aichi declaring the 120+30 day
period mandatory and jurisdictional, thus reversing BIR Ruling No. DA-489-03. (HEDCOR, INC. vs.
COMMISSIONER OF INTERNAL REVENUE, G.R. No. 207575. JULY 15, 2015)

For failure of Silicon to comply with the provisions of Section 112(C) of the NIRC, its judicial claims
for tax refund or credit should have been dismissed by the CTA for lack of jurisdiction. The Court
stresses that the 120/30-day prescriptive periods are mandatory and jurisdictional, and are not mere
technical requirements. (SILICON PHILIPPINES, INC. (FORMERLY INTEL PHILIPPINES
MANUFACTURING, INC.) vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 173241, MARCH
25, 2015, J. LEONARDO-DE CASTRO)
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Gotescos relentless refusal to transfer registered ownership of the Ever Ortigas Commercial Complex
to PNB constitutes proof enough that Gotesco will not do any act inconsistent with its claim of
ownership over the foreclosed asset, including claiming the creditable tax imposed on the foreclosure
sale as tax credit and utilizing such amount to offset its tax liabilities. To do such would run roughshod
over Gotescos firm stance that PNBs foreclosure on the mortgage was invalid and that it remained
the owner of the subject property. While perhaps it may be necessary to prove that the taxpayer did
not use the claimed creditable withholding tax to pay for his/its tax liabilities, there is no basis in law
or jurisprudence to say that BIR Form No. 2307 is the only evidence that may be adduced to prove
such non-use. (PHILIPPINE NATIONAL BANK vs. COMMISSIONER OF INTERNAL REVENUE, G.R.
No. 206019, MARCH 18, 2015, J. VELASCO JR.)

The CIR has 120 days from the date of submission of complete documents in support of the
administrative claim within which to decide whether to grant a refund or issue a tax credit
certificate. In case of failure on the part of the CIR to act on the application within the 120-day period
prescribed by law, the taxpayer has only has 30 days after the expiration of the 120-day period to
appeal the unacted claim with the CTA. Since petitioners judicial claim was filed before the CTA only
way beyond the mandatory 120+30 days to seek judicial recourse, such non-compliance with the
mandatory period of 30 days is fatal to its refund claim on the ground of prescription. Consequently,
the CTA has no jurisdiction over its judicial appeal considering that its Petition for Review was filed
out of time. Consequently, the claim for refund must be denied. (NIPPON EXPRESS (PHILIPPINES)
CORP. vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 185666, FEBRUARY 04, 2015, J.
PEREZ)

In Reconciling the pronouncements in the Aichi and San Roque cases, the rule must therefore be that
during the period December 10, 2003 (when BIR Ruling No. DA-489-03 was issued) to October 6,
2010 (when the Aichi case was promulgated), taxpayers-claimants need not observe the 120-day
period before it could file a judicial claim for refund of excess input VAT before the CTA. Before and
after the aforementioned period (i.e., December 10, 2003 to October 6, 2010), the observance of the
120-day period is mandatory and jurisdictional to the filing of such claim. (PANAY POWER
CORPORATION vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 203351, JANUARY 21,
2015, J. PERLAS-BERNABE)

A VAT-registered taxpayer need not wait for the lapse of the 120-day period to file a judicial claim
for unutilized VAT inputs before the CTA when the claim was filed on December 10, 2003 up to
October 6, 2010. If the claim is filed within those dates, the same shall not be considered prematurely
filed. In this case, records disclose that petitioner filed its administrative and judicial claims for
refund/credit of its input VAT in CTA Case No. 8082 on December 28, 2009 and March 30, 2010,
respectively, or during the period when BIR Ruling No. DA-489-03 was in place, i.e., from December
10, 2003 to October 6, 2010. As such, it need not wait for the expiration of the 120-day period before
filing its judicial claim before the CTA, and hence, is deemed timely filed. In view of the foregoing,
both the CTA Division and the CTA En Banc erred in dismissing outright petitioners claim on the
ground of prematurity. (MINDANAO II GEOTHERMAL PARTNERSHIP vs. COMMISSIONER OF
INTERNAL REVENUE, G.R. No. 204745, DECEMBER 08, 2014, J. PERLAS-BERNABE)

In 1993, the BIR issued against respondent assessment notice for deficiency income tax for 1989. A
waiver of the defense of prescription was executed but it was not signed by the Commissioner or any
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of his authorized representatives and did not state the date of acceptance. The Court held that the
Commissioners right to collect has prescribed. The period to assess and collect deficiency taxes may
be extended only upon a written agreement between the Commissioner and the taxpayer prior to the
expiration of the three-year prescribed period. The BIR cannot claim the benefits of extending the
period when it was the BIRs inaction which is the proximate cause of the defects of the waiver.
(COMMISSIONER OF INTERNAL REVENUE vs. THE STANLEY WORKS SALES (PHILS.),
INCORPORATED, G.R. No. 187589, DECEMBER 03, 2014, CJ. SERENO)

CBK Power filed its judicial claim for refund/credit just 20 days after it filed its administrative claim.
CTA En Banc dismissed the case for lack of jurisdiction as it failed to observe the mandatory and
jurisdictional 120-day period provided under Section 112 (D) of the National Internal Revenue Code.
The Court found that the CTA En Banc was incorrect. The Court recognized an exception in which the
existing BIR Ruling applicable to this case in which it held that taxpayer-claimant need not wait for
the lapse of the 120-day period before it could seek judicial relief. (CBK POWER COMPANY LIMITED
vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 198928, DECEMBER 03, 2014, J. PERLAS-
BERNABE)
As an exception to the mandatory and jurisdictional nature of the 120+ 30 day period, judicial claims
filed between December 10, 2003 or from the issuance of BIR Ruling No. DA-489-03, up to October
6, 2010 or the reversal of the ruling in Aichi, need not wait for the lapse of the 120+ 30 day period in
consonance with the principle of equitable estoppel. In the present case, Taganito filed its judicial
claim with the CTA on February 19, 2004, clearly within the period of exception of December I 0,
2003 to October 6, 20 I 0. Its judicial claim was, therefore, not prematurely filed and should not have
been dismissed by the CTA En Banc. (TAGANITO MINING CORPORATION vs. COMMISSIONER OF
INTERNAL REVENUE, G.R. No. 198076, NOVEMBER 19, 2014, J. MENDOZA)
As a general rule, a taxpayer-claimant needs to wait for the expiration of the one hundred twenty
(120)-day period before it may be considered as "inaction" on the part of the Commissioner of
Internal Revenue (CIR). Thereafter, the taxpayer-claimant is given only a limited period of thirty (30)
days from said expiration to file its corresponding judicial claim with the CTA. However, with the
exception of claims made during the effectivity of BIR Ruling No. DA-489-03 (from 10 December 2003
to 5 October 2010), AT&T Communications has indeed properly and timely filed its judicial claim
covering the Second, Third, and Fourth Quarters of taxable year 2003, within the bounds of the law
and existing jurisprudence. The VAT invoice is the seller's best proof of the sale of the goods or
services to the buyer while the VAT receipt is the buyer's best evidence of the payment of goods or
services received from the seller. Thus, the High Court concluded that VAT invoice and VAT receipt
should not be confused as referring to one and the same thing. Certainly, neither does the law intend
the two to be used interchangeably. (AT&T COMMUNICATIONS SERVICES PHILIPPINES, INC. vs.
COMMISSIONER OF INTERNAL REVENUE, G.R. No. 185969, NOVEMBER 19, 2014, J. PEREZ)
Aichi filed an application for tax credit/refund with the BIR on March 29, 2005. On 31 March 2005,
respondent filed judicial claim before the CTA. BIR contends that Aichi failed to observe the 120-day
reglementary period provided by NIRC for the CIR to act on the claim. In this issue the Supreme court
ruled that the Court agree with petitioner that the judicial claim was prematurely filed on 31 March
2005, since respondent failed to observe the mandatory 120day waiting period to give the CIR an
opportunity to act on the administrative claim. However, the Court ruled in San Roque that BIR
Ruling No. DA-489-03 allowed the premature filing of a judicial claim, which means non-exhaustion
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of the 120-day period for the Commissioner to act on an administrative claim. All taxpayers can rely
on BIR Ruling No. DA-489-03 from the time of its issuance on 10 December 2003 up to its reversal
by this Court in Aichi on 6 October 2010, where this Court held that the 120+30 day periods are
mandatory and jurisdictional. Therefore, respondent's filing of the judicial claim barely two days
after the administrative claim is acceptable, as it fell within the period during which the Court
recognized the validity of BIR Ruling No. DA-489-03. (COMMISSIONER OF INTERNAL REVENUE vs.
AICHI FORGING COMPANY OF ASIA, INC., G.R. No. 183421, OCTOBER 22, 2014, CJ SERENO)
Section 112 (D) (now renumbered as Section 112[C]) of RA 8424, which is explicit on the mandatory
and jurisdictional nature of the 120+30-day period, was already effective on January 1, 1998. That
being said, and notwithstanding the fact that respondent's administrative claim had been timely filed,
the Court is nonetheless constrained to deny the averred tax refund or credit, as its judicial claim
therefore was filed beyond the 120+30-day period, and, hence - as earlier stated - deemed to be filed
out of time. As the records would show, the CIR had 120 days from the filing of the administrative
claim on July 21, 1999, or until November 18, 1999, to decide on respondent's application. Since the
CIR did not act at all, respondent had until December 18, 1999, the last day of the 30-day period, to
file its judicial claim. Respondent filed its petition for review with the CTA only on January 9, 2001
and, thus, was one (1) year and 22 days late. (COMMISSIONER OF INTERNAL REVENUE vs.
BURMEISTER AND WAIN SCANDINAVIAN CONTRACTOR MINDANAO, INC., G.R. No. 190021,
OCTOBER 22, 2014, J. PERLAS-BERNABE)
The Atlas doctrine, which held that claims for refund or credit of input VAT must comply with the
two-year prescriptive period under Sec. 229, should be effective only from its promulgation on June
8, 2007 until its abandonment on [September 12, 2008] in Mirant. The Atlas doctrine was limited to
the reckoning of the two-year prescriptive period from the date of payment of the output VAT. The
Mirant ruling, which abandoned the Atlas doctrine, adopted the verba legis rule, thus applying Sec.
112(A) in computing the two-year prescriptive period in claiming refund or credit of input VAT. Since
July 23, 2008 falls within the window of effectivity of Atlas, CBKs administrative claim for the second
quarter of 2006 was filed on time considering that it filed the original VAT return for the second
quarter on July 25, 2006. (CBK POWER COMPANY LIMITED vs. COMMISSIONER OF INTERNAL
REVENUE, G.R. No. 202066, SEPTEMBER 30, 2014, J. LEONEN)
As a general rule, compliance with the 120-day period stated in Section 112(D) of NIRC is mandatory.
However, a VAT-registered taxpayer claiming refund for input VAT may not wait for the lapse of the
120-day period when the claim is filed between December 10, 2003 (the time of promulgation of BIR
Ruling No. DA-489-03) to October 6, 2010 (the time of promulgation of the Aichi case). (TAGANITO
MINING CORPORATION vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 197591, JUNE 18,
2014, J. PERLAS-BERNABE)
When a taxpayer seeking refund or tax credit under VAT files a judicial claim beyond the 30-day
period provided by the law, the same shall be dismissed for lack of jurisdiction. A taxpayer seeking
refund or tax credit under VAT must strictly follow the 120+30 rule to be entitled thereof,
otherwise, the claim shall be barred. In the present case, the respondent filed its administrative claim
on May 30, 2003. The petitioner CIR therefore had only until September 27, 2003 to decide the claim,
and following the petitioners inaction, the respondent had until October 27, 2003, the last day of the
30-day period to file its judicial claim. However, the respondent filed its judicial claim with the CTA
only on March 31, 2004 or 155 days late. Clearly, the respondent's judicial claim has prescribed and
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the CTA did not acquire jurisdiction over the claim. (COMMISSIONER OF INTERNAL REVENUE vs.
MINDANAO II GEOTHERMAL PARTNERSHIP, G.R. No. 189440, JUNE 18, 2014, J. VILLARAMA,
JR.)
The mandatory rule is that a judicial claim must be filed with the CTA within thirty (30) days from
the receipt of the Commissioners decision denying the administrative claim or from the expiration
of the 120day period without any action from the Commissioner. Otherwise, said judicial claim shall
be considered as filed out of time. (COMMISSIONER OF INTERNAL REVENUE, vs. SILICON
PHILIPPINES, INC. (FORMERLY INTEL PHILIPPINES MANUFACTURING, INC.), G.R. No. 169778,
March 12, 2014, J. PEREZ)
What is important, as far as the present cases are concerned, is that the mere filing by a taxpayer of
a judicial claim with the CTA before the expiration of the 120-day period cannot operate to divest the
Commissioner of his jurisdiction to decide an administrative claim within the 120-day mandatory
period, unless the Commissioner has clearly given cause for equitable estoppel to apply as expressly
recognized in Section 246 of the Tax Code. (COMMISSIONER OF INTERNAL REVENUE vs. TEAM
SUAL CORPORATION (formerly MIRANT SUAL CORPORATION, G.R. No. 194105 February 5,
2014, J. REYES)
Under Section 112(C) of the NIRC, a taxpayer-claimant may only file a petition for review with the
CTA within 30 days from either: (1) the receipt of the decision of the CIR denying, in full or in part,
the claim for refund/tax credit; or (2) the lapse of the 120-day period given to the CIR to decide the
claim for refund/tax credit. The 120-day mandatory period may extend beyond the two-year
prescriptive period for filing a claim for refund/tax credit under Section 112(A) of the NIRC.
Consequently, the30-day period given to the taxpayer-claimant likewise need not fall under the two-
year prescriptive period. What matters is that the administrative claim for refund/tax credit of
unutilized input VAT is filed with the BIR within the two-year prescriptive period. (COMMISSIONER
OF INTERNAL REVENUE vs. TEAM SUAL CORPORATION (formerly MIRANT SUAL
CORPORATION), G.R. No. 194105, FEBRUARY 5, 2014, J. REYES)
TPI filed its third and fourth quarterly VAT returns for 2001 on October 25, 2001 and January 25,
2002, respectively. It then filed an administrative claim for refund of its unutilized input VAT for the
third and fourth quarters of 2001 on September 30, 2003. Thus, the CIR had 120 days or until January
28, 2004, after the submission of TPIs administrative claim and complete documents in support of
its application, within which to decide on its claim. Then, it is only after the expiration of the 120-day
period, if there is inaction on the part of the CIR, where TPI may elevate its claim with the CTA within
30 days. In the present case, however, it appears that TPIs judicial claims for refund of its unutilized
input VAT covering the third and fourth quarters of 2001 were prematurely filed on October 24, 2003
and January 22, 2004, respectively. However, although TPIs judicial claim for the fourth quarter of
2001 has been filed prematurely, the most recent pronouncements of the Court provide for a window
wherein the same may be entertained. As held in the San Roque ponencia, strict compliance with the
120+30 day mandatory and jurisdictional periods is not necessary when the judicial claims are filed
between December 10, 2003 (issuance of BIR Ruling No. DA-489-03 which states that the taxpayer
need not wait for the 120-day period to expire before it could seek judicial relief) to October 6, 2010
(promulgation of the Aichi doctrine). Clearly, therefore, TPIs refund claim of unutilized input VAT
for the third quarter of 2001 was denied for being prematurely filed with the CTA, while its refund
claim of unutilized input VAT for the fourth quarter of 2001 may be entertained since it falls within
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the exception provided in the Courts most recent rulings. (COMMISSIONER OF INTERNAL
REVENUE vs. TOLEDO POWER, INC, G.R. No. 183880 JANUARY 20, 2014, J. PERALTA)
The taxpayer can file the appeal in one of two ways: (1) file the judicial claim within thirty days after
the Commissioner denies the claim within the 120-day period, or (2) file the judicial claim within
thirty days from the expiration of the 120-day period if the Commissioner does not act within the
120-day period. Mindanao II filed its administrative claim for refund or credit for the second, third,
and fourth quarters of 2004 on 6 October 2005. The CIR, therefore, had a period of 120 days, or until
3 February 2006, to act on the claim. The CIR, however, failed to do so. Mindanao II then could treat
the inaction as a denial and appeal it to the CTA within 30 days from 3 February 2006, or until 5
March 2006. Mindanao II, however, filed a Petition for Review only on 21 July 2006, 138 days after
the lapse of the 30-day period on 5 March 2006. The judicial claim was therefore filed late. The CTA
therefore lost jurisdiction over Mindanao Ils claims for refund or credit. (COMMISSIONER OF
INTERNAL REVENUE vs. MINDANAO II GEOTHERMAL PARTNERSHIP G.R. No. 1914498
JANUARY 15, 2014, CJ. SERENO)
While petitioner filed its administrative and judicial claims during the period of applicability of BIR
Ruling No. DA-489-03, it cannot claim the benefit of the exception period as it did not file its judicial
claim prematurely, but did so long after the lapse of the 30-day period following the expiration of the
120-day period. Again, BIR Ruling No. DA-489-03 allowed premature filing of a judicial claim, which
means non-exhaustion of the 120-day period for the Commissioner to act on an administrative claim,
but not its late filing. For failure of petitioner to comply with the 120+30 day mandatory and
jurisdictional period, petitioner lost its right to claim a refund or credit of its alleged excess input
VAT. (CBK POWER COMPANY LIMITED vs. COMMISSIONER OF INTERNAL REVENUE, G.R.
Nos.198729-30 JANUARY 15, 2014, CJ. SERENO)
In this case, petitioner filed its judicial claim for refund on April 18, 2007 or after the issuance of BIR
Ruling No. DA-489-03 on December 10, 2003 but before October 6, 2010, the date when the Aichi
case was promulgated. BIR Ruling No. DA-489-03 which is a general interpretative rule, was issued
in response to a query made, not by a particular taxpayer, but by a government agency tasked with
processing tax refunds and credits, that is, the One Stop Shop Inter-Agency Tax Credit and Drawback
Center of the Department of Finance. BIR ruling held that the taxpayer did not wait for the lapse of
the 120-day period to file for a judicial claim for refund. In the Aichi case, the Court ruled that the
120-30-day period in Section 112 (C) of the NIRC is mandatory and its non-observance is fatal to the
filing of a judicial claim with the CTA. In this case, the Court explained that if after the 120-day
mandatory period, the Commissioner of Internal Revenue (CIR) fails to act on the application for tax
refund or credit, the remedy of the taxpayer is to appeal the inaction of the CIR to the CTA within
thirty (30) days. The judicial claim, therefore, need not be filed within the two-year prescriptive
period but has to be filed within the required 30-day period after the expiration of the 120 days. Thus,
even though petitioners judicial claim was prematurely filed without waiting for the expiration of
the 120-day mandatory period, the CTA may still take cognizance of the instant case as it was filed
within the period exempted from the 120-30-day mandatory period. (TEAM ENERGY
CORPORATION (formerly MIRANT PAGBILAO CORP.) vs. COMMISSIONER OF INTERNAL
REVENUE, G.R. No. 190928 JANUARY 13, 2014, J. PERALTA)
GOVERNMENT REMEDIES
Page 44 of 53

ADMINISTRATIVE REMEDIES
Section 229 of Presidential Decree (P.D.) No. 1158, the law in effect at the time of the disputed
assessment, stated that prior resort to the administrative remedies was necessary; otherwise, the
assessment would attain finality. Section 230 of P.D. No. 1158 allowed Alcantara to file his claim for
refund for the erroneously or illegally paid taxes. In this regard, such claim for refund was also a
prerequisite before any resort to the courts could be made to recover the erroneously or illegally
paid taxes. Yet, Alcantara immediately invoked the authority of the courts to protect his rights instead
of first going to the Commissioner of Internal Revenue for redress of his concerns about the
assessment and collection of taxes. His judicial recourse thus suffered from fatal prematurity because
his doing so rendered the assessment final. (DEMETRIO R. ALCANTARA vs. REPUBLIC OF THE
PHILIPPINES, G.R. No. 192536, March 15, 2017, BERSAMIN, J.)
The Supreme Court has upheld the validity of the BIR ruling, because the power to interpret rules
and regulations is not exclusive and may be delegated by the CIR to the Deputy Commissioner.
(PROCTOR AND GAMBLE ASIA PTE. LTD. vs. COMMISSIONER OF INTERNAL REVENUE, GR
204277, May 30, 2016, BRION, J.)
CBK Power raised the lone issue of whether or not an ITAD ruling is required before it can avail of
the preferential tax rate. On the other hand, the Commissioner claimed that CBK Power failed to
exhaust administrative remedies when it filed its petitions before the CTA First Division, and that
said petitions were not filed within the two-year prescriptive period for initiating judicial claims for
refund. The Court categorically held that the BIR should not impose additional requirements that
would negate the availment of the reliefs provided for under international agreements, especially
since said tax treaties do not provide for any prerequisite at all for the availment of the benefits under
said agreements. Nowhere and in no wise does the law imply that the Collector of Internal Revenue
must act upon the claim, or that the taxpayer shall not go to court before he is notified of the
Collectors action. (CBK POWER COMPANY LIMITED vs. COMMISSIONER INTERNAL REVENUE,
G.R. Nos. 193383-84, JANUARY 14, 2015, J. PERLAS-BERNABE)
The issues raised before the Panel of Voluntary Arbitrators are: (1) whether the cash conversion of
the gasoline allowance shall be subject to fringe benefit tax or the graduated income tax rate on
compensation; and (2) whether the company wrongfully withheld income tax on the converted gas
allowance. The Voluntary Arbitrator has no competence to rule on the taxability of the gas allowance
and on the propriety of the withholding of tax. These issues are clearly tax matters, and do not involve
labor disputes. To be exact, they involve tax issues within a labor relations setting as they pertain to
questions of law on the application of Section 33 (A) of the NIRC. They do not require the application
of the Labor Code or the interpretation of the MOA and/or company personnel policies. Furthermore,
the company and the union cannot agree or compromise on the taxability of the gas allowance.
Taxation is the States inherent power; its imposition cannot be subject to the will of the parties. If
the union disputes the withholding of tax and desires a refund of the withheld tax, it should have filed
an administrative claim for refund with the CIR. Paragraph 2, Section 4 of the NIRC expressly vests
the CIR original jurisdiction over refunds of internal revenue taxes, fees or other charges, penalties
imposed in relation thereto, or other tax matters. (HONDA CARS PHILIPPINES, INC. vs. HONDA
CARS TECHNICAL SPECIALIST AND SUPERVISORS UNION, G.R. No. 204142, NOVEMBER 19,
2014, J. BRION)
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There could be no presumption of the regularity of any administrative action which resulted in
depriving a taxpayer of his property through a tax sale. This is an exception to the rule that
administrative proceedings are presumed to be regular. This jurisprudential tenor clearly
demonstrates that the burden to prove compliance with the validity of the proceedings leading up to
the tax delinquency sale is incumbent upon the buyer or the winning bidder, which, in this case, is
Agojo. This is premised on the rule that a sale of land for tax delinquency is in derogation of property
and due process rights of the registered owner. In order to be valid, the steps required by law must
be strictly followed. Agojo must be reminded that the requirements for a tax delinquency sale under
the LGC are mandatory. Strict adherence to the statutes governing tax sales is imperative not only for
the protection of the taxpayers, but also to allay any possible suspicion of collusion between the buyer
and the public officials called upon to enforce the laws. (CORPORATE STRATEGIES DEVELOPMENT
CORP. and RAFAEL R. PRIETO vs. NORMAN A. AGOJO, G.R. No. 208740, NOVEMBER 19, 2014, J.
MENDOZA)

Agriex Co. foreign corporation alleges that the Bureau of Customs exclusive original jurisdiction over
actual and physical possession of foreign shipments and thus RTC has no jurisdiction over such. The
court ruled that it is well settled that the Collector of Customs has exclusive jurisdiction over seizure
and forfeiture proceedings, and regular courts cannot interfere with his exercise thereof or stifle or
put it at naught. The Collector of Customs sitting in seizure and forfeiture proceedings has exclusive
jurisdiction to hear and determine all questions touching on the seizure and forfeiture of dutiable
goods. Regional trial courts are devoid of any competence to pass upon the validity or regularity of
seizure and forfeiture proceedings conducted by the BOC and to enjoin or otherwise interfere with
these proceedings. Regional trial courts are precluded from assuming cognizance over such matters
even through petitions for certiorari, prohibition or mandamus. (AGRIEX CO., LTD vs. HON. TITUS
B. VILLANUEVA and HON. BILLY C. BIBIT G.R. No. 158150, SEPTEMBER 10, 2014, J. BERSAMIN)

The CIR categorically admitted that it failed to formally offer the Preliminary Assessment Notices as
evidence. Worse, it advanced no justifiable reason for such fatal omission. Instead, it merely alleged
that the existence and due execution of the Preliminary Assessment Notices were duly tackled by
CIRs witnesses. We hold that such is not sufficient to seek exception from the general rule requiring
a formal offer of evidence, since no evidence of positive identification of such Preliminary Assessment
Notices by petitioners witnesses was presented. (COMMISSIONER OF INTERNAL REVENUE vs.
UNITED SALVAGE AND TOWAGE (PHILS.), INC., G.R. No. 197515, JULY 2, 2014, J. PERALTA)
JUDICIAL REMEDIES

In order for the CTA En Banc to take cognizance of an appeal via a petition for review, a timely motion
for reconsideration or new trial must first be filed with the CTA Division that issued the assailed
decision or resolution. Failure to do so is a ground for the dismissal of the appeal as the word "must"
indicates that the filing of a prior motion is mandatory, and not merely directory. The same is true in
the case of an amended decision. Section 3, Rule 14 of the amended CTA rules defines an amended
decision as any action modifying or reversing a decision of the Court en bane or in Division. As
explained in CE Luzon Geothermal Power Company, Inc. v. Commissioner of Internal Revenue, an
amended decision is a different decision, and thus, is a proper subject of a motion for reconsideration.
In this case, the CIR's failure to move for a reconsideration of the Amended Decision of the CTA
Division is a ground for the dismissal of its Petition for Review before the CTA En Banc. Thus, the CTA
En Banc did not err in denying the CIR's appeal on procedural grounds. Due to this procedural lapse,
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the Amended Decision has attained finality insofar as the CIR is concerned. The CIR, therefore, may
no longer question the merits of the case before this Court. (ASIATRUST DEVELOPMENT BANK,
INC. vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No. 201530, APRIL 19, 2017, DEL
CASTILLO, J.)

An application for tax abatement is considered approved only upon the issuance of a termination
letter: Section 204(B) of the 1997 National lnternal Revenue Code empowers the CIR to abate or
cancel a tax liability. Based on the guidelines, the last step in the tax abatement process is the issuance
of the termination letter. The presentation of the termination letter is essential as it proves that the
taxpayer's application for tax abatement has been approved. Thus, without a termination letter, a tax
assessment cannot be considered closed and terminated. (ASIATRUST DEVELOPMENT BANK, INC.
vs. COMMISSIONER OF INTERNAL REVENUE, G.R. NO. 201530, APRIL 19, 2017, DEL CASTILLO,
J.)

The complaint was brought to assail the assessment and collection made by the Commissioner of
Internal Revenue. Based on Republic Act No. 1125, prior to its amendment by Republic Act No. 9282,
the CTA had exclusive appellate jurisdiction over the appeal of the decisions of the Commissioner of
Internal Revenue. Accordingly, the CA correctly dismissed Alcantara's appeal on the ground of lack
of jurisdiction to entertain the same. The erroneous appeal deserved no fate but dismissal. Section 2,
Rule 50 of the Rules of Court expressly states: "An appeal erroneously taken to the Court of Appeals
shall not be transferred to the appropriate court but shall be dismissed outright." (DEMETRIO R.
ALCANTARA vs. REPUBLIC OF THE PHILIPPINES, G.R. No. 192536 MARCH 15, 2017, BERSAMIN,
J.)

We deem it proper to clarify the last sentence in the decision that "[i]t did not matter where the RTC
decision was appealed, whether before the C[ourt Of A[ppeals] or the C[ourt of T[ax] A[ppeals]."
Republic Act No. 9282, which amended Republic Act No. 1125, took effect on April 23, 2004, and
significantly expanded the extent and scope of the cases that the Court of Tax Appeals was tasked to
hear and adjudicate. Under Section 7, paragraph (a)(3), the Court of Tax Appeals is vested with the
exclusive appellate jurisdiction over, among others, appeals from the "decisions, orders or
resolutions of the Regional Trial Courts in local tax cases originally decided or resolved by them in
the exercise of their original or appellate jurisdiction." The case a quo is a local tax case that is within
the exclusive appellate jurisdiction of the Court of Tax Appeals. (NATIONAL POWER CORPORATION
vs. PROVINCIAL GOVERNMENT OF BATAAN, G.R. 180654, MARCH 6, 2017, LEONEN, J.)

The CTA is a highly specialized body that reviews tax cases and conducts trial de novo. Thus, without
any showing that the findings of the CTA are unsupported by substantial evidence, its findings are
binding on the Court. (COMMISSIONER OF INTERNAL REVENUE AND COMMISSIONER OF
CUSTOMS vs. PHILIPPINE AIRLINES, G.R. No. 215705-07 FEBRUARY 22, 2017, PERALTA, J.)

The Revised Rules of the CTA and even the Rules of Court which apply suppletorily thereto provide
for no instance in which the en banc may reverse, annul or void a final decision of a division. Verily,
the Revised Rules of the CTA provide(s) for no instance of an annulment of judgment at all. On the
other hand, the Rules of Court, through Rule 47, provides, with certain conditions, for annulment of
judgment done by a superior court, like the Court of Appeals, against the final judgment, decision or
ruling of an inferior court, which is the Regional Trial Court, based on the grounds of extrinsic fraud
and lack of jurisdiction. The Regional Trial Court, in turn, also is empowered to, upon a similar action,
Page 47 of 53

annul a judgment or ruling of the Metropolitan or Municipal Trial Courts within its territorial
jurisdiction. But, again, the said Rules are silent as to whether a collegial court sitting en banc may
annul a final judgment of its own division. As earlier explained, the silence of the Rules may be
attributed to the need to preserve the principles that there can be no hierarchy within a collegial
court between its divisions and the en banc, and that a courts judgment, once final, is immutable. A
direct petition for annulment of a judgment of the CTA to the Supreme Court, meanwhile, is likewise
unavailing, for the same reason that there is no identical remedy with the High Court to annul a final
and executory judgment of the Court of Appeals. RA No. 9282, Section 1 puts the CTA on the same
level as the Court of Appeals, so that if the latters final judgments may not be annulled before the
Supreme Court, then the CTAs own decisions similarly may not be so annulled. And more
importantly, it has been previously discussed that annulment of judgment is an original action, yet, it
is not among the cases enumerated in the Constitution, Article VIII, Section 5, over which the Supreme
Court exercises original jurisdiction. Annulment of judgment also often requires an adjudication of
facts, a task that the Court loathes to perform, as it is not a trier of facts. Instead, what remained as a
remedy for the petitioner was to file a petition for certiorari under Rule 65, which could have been
filed as an original action before this Court and not before the CTA en banc. xxx In any event,
petitioners failure to avail of this remedy and mistake in filing of the wrong action are fatal to its case
and renders and leaves the CTA First Divisions decision as indeed final and executory. By the time
the instant petition for review was filed by petitioner with this Court, more than sixty (60) days have
passed since petitioners alleged discovery of its loss in the case as brought about by the alleged
negligence or fraud of its counsel. (COMMISSIONER OF INTERNAL REVENUE vs. KEPCO ILIJAN
CORPORATION G.R. No. 199422, JUNE 21, 2016, J. PERALTA, EN BANC)

Despite the amendments to the law, the Court still holds that the CTA has ample authority to issue
injunctive writs to restrain the collection of tax and to even dispense with the deposit of the amount
claimed or the filing of the required bond, whenever the method employed by the CIR in the collection
of tax jeopardizes the interests of a taxpayer for being patently in violation of the law. Such authority
emanates from the jurisdiction conferred to it not only by Section 11 of R.A. No. 1125, but also by
Section 7 of the same law. From all the foregoing, it is clear that the authority of the courts to issue
injunctive writs to restrain the collection of tax and to dispense with the deposit of the amount
claimed or the filing of the required bond is not simply confined to cases where prescription has set
in. As explained by the Court, whenever it is determined by the courts that the method employed by
the Collector of Internal Revenue in the collection of tax is not sanctioned by law, the bond
requirement under Section 11 of R.A. No. 1125 should be dispensed with. The purpose of the rule is
not only to prevent jeopardizing the interest of the taxpayer, but more importantly, to prevent the
absurd situation wherein the court would declare that the collection by the summary methods of
distraint and levy was violative of law, and then, in the same breath require the petitioner to deposit
or file a bond as a prerequisite for the issuance of a writ of injunction. (SPOUSES EMMANUEL
PACQUIAO AND JINKEE PACQUIAO vs. COURT OF TAX APPEALS, G.R. NO. 213994, APRIL 16,
2016, J. MENDOZA)

Under Section 112 of the NIRC, if the administrative claim for tax credit or refund of input taxes is
not acted upon by the CIR within 120 days from the date of submission of complete documents in
support of the application, the taxpayer affected may appeal the unacted claim with the CTA within
30 days from the expiration of the 120-day period. In Aichi, this Court ruled that observance of the
120- and 30-day periods is crucial in the filing of an appeal before the CTA. By "crucial," this Court
meant that its observance is jurisdictional and mandatory, not merely permissive. Indeed, Aichi is the
Page 48 of 53

prevailing doctrine on the matter of mandatory compliance with the 120- and 30-day periods in the
filing of judicial claims of tax credit or refund before the CTA. However, in the manner of most rules,
the Aichi Doctrine is also subject to exceptions. In accordance with the equitable estoppel principle
under Section 246 of the NIRC, we ruled in San Roque-Taganito that there are exceptions to the strict
rule that compliance with the Aichi Doctrine is mandatory and jurisdictional, one of which is BIR
Ruling No. DA-489-03. If the CIR issues a ruling, either a specific one applicable to a particular
taxpayer or a general interpretative rule applicable to all taxpayers, and, as a result, misleads the
taxpayers affected by the rule, into filing prematurely judicial claims with the CTA, the CIR cannot be
allowed to later on question the CTA's assumption of jurisdiction over such claim. Since then, this
Court has consistently adopted the ruling in San Roque-Taganito in holding that BIR Ruling No. DA-
489-03 is an exception to the Aichi Doctrine. We see no reason to disturb what is now a settled ruling.
(PROCTOR AND GAMBLE ASIA PTE. LTD. vs. COMMISSIONER OF INTERNAL REVENUE, GR
204277, MAY 30, 2016, BRION, J.)

Concededly, there is no clear statement under R.A. No. 1125, the amendatory R.A. No. 9282, let alone
in the Constitution, that the CTA has original jurisdiction over a petition for certiorari. A petition
before the CTA may only be made after a whole or partial denial of the protest by the CIR or the CIR's
authorized representative. When PAGCOR filed its petition before the CTA on 11 March 2009, there
was still no denial of PAGCOR's protest by either the RD or the CIR. PAGCOR has clearly failed to
comply with the requisites in disputing an assessment as provided by Section 228 and Section 3.1.5.
(PHILIPPINE AMUSEMENT AND GAMING CORPORATION vs. BUREAU OF INTERNAL REVENUE,
G.R. No. 208731. JANUARY 27, 2016)

While it is true that the CTA Division has the prerogative to grant a motion to withdraw under the
authority of the foregoing legal provisions, the attendant circumstances in this case should have
incited it to act otherwise. The primary reason, however, that militates against the granting of the
motion to withdraw is the fact that the CTA Division, in its August 10, 2011 Decision, had already
determined that Nippon was only entitled to refund the reduced amount of P2,614,296.84 since it
failed to prove that the recipients of its services were non-residents "doing business outside the
Philippines"; hence, Nippon's purported sales therefrom could not qualify as zero-rated sales,
necessitating the reduction in the amount of refund claimed. Markedly different from this is the BIR'
s determination that Nippon should receive P21,675,128.91 as per the July 27, 2011 Tax Credit
Certificate, which is, in all, P19,060,832.07 larger than the amount found due by the CTA Division.
Therefore, as aptly pointed out by Associate Justice Teresita J. Leonardo-De Castro during the
deliberations on this case, the massive discrepancy alone between the administrative and judicial
determinations of the amount to be refunded to Nippon should have already raised a red flag to the
CTA Division. Clearly, the interest of the government, and, more significantly, the public, will be
greatly prejudiced by the erroneous grant of refund -at a substantial amount at that -in favor of
Nippon. Hence, under these circumstances, the CTA Division should not have granted the motion to
withdraw. (COMMISSIONER OF INTERNAL REVENUE vs. NIPPON EXPRESS (PHILS.)
CORPORATION, G.R. No. 212920. SEPTEMBER 16, 2015)

The Court thus declares that the CA's original jurisdiction over a petition for certiorari assailing the
DOJ resolution in a preliminary investigation involving tax and tariff offenses was necessarily
transferred to the CTA pursuant to Section 7 of R.A. No. 9282, and that such petition shall be governed
by Rule 65 of the Rules of Court, as amended. Accordingly, it is the CTA, not the CA, which has
jurisdiction over the petition for certiorari assailing the DOJ resolution of dismissal of the BOC's
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complaint-affidavit against private respondents for violation of the TCCP. (BUREAU OF CUSTOMS
vs. THE HONORABLE AGNES DEVANADERA, et al.,G.R. No. 193253. SEPTEMBER 8, 2015)

Under Section 3, Rule 14 of the Revised Rules of the Court of Tax Appeals, an amended decision is
issued when there is any action modifying or reversing a decision of the CTA En Banc or in Division.
Pursuant to these parameters, it is clear that the CIRs motions for partial reconsideration i.e., (a)
motion for partial reconsideration of the June 24, 2009 Decision; and (b) motion for partial
reconsideration of the January 19, 2010 Amended Decision assailed separate and distinct decisions
that were rendered by the CTA Division. Notably, its amended decision modified and increased CE
Luzons entitlement to a refund or tax credit certificate in the amount of -17,277,938.47. Essentially,
it was therefore a different decision and, hence, the proper subject of a motion for reconsideration
anew on the part of the CIR. Thus, CE Luzons procedural objection must fail. (CE LUZON
GEOTHERMAL POWER COMPANY, INC. vs. COMMISSIONER OF INTERNAL REVENUE, G.R. No.
200841-42. AUGUST 26, 2015)

It is within the CTA's sound judicial discretion to give party-litigants every opportunity to properly
present their conflicting claims on the merits of the controversy without resorting to technicalities.
It should always be predicated on the consideration that more than the mere convenience of the
courts or of the parties of the case, the ends of justice and fairness would be served thereby. Courts
should be liberal in setting aside orders of default, for default judgments are frowned upon, and
unless it clearly appears that the reopening of the case is intended for delay, it is best that trial courts
give both parties every chance to fight their case fairly and in the open, without resort to technicality.
(COMMISSIONER OF INTERNAL REVENUE vs. COURT OF TAX APPEALS AND CB POWER
COMPANY LIMITED, G.R. Nos. 203054-55. JULY 29, 2015)

Petron admitted to not having filed a protest of the assessment before the customs collector and
elevating a possible adverse ruling therein to the COC, reasoning that such a procedure would be
costly and impractical, and would unjustly delay the resolution of the issues which, being purely legal
in nature anyway, were also beyond the authority of the customs collector to resolve with finality.
This admission is at once decisive of the issue of the CTA's jurisdiction over the petition. There being
no protest ruling by the customs collector that was appealed to the COC, the filing of the petition
before the CTA was premature as there was nothing yet to review. (COMMISSIONER OF INTERNAL
REVENUE vs. COURT OF TAX APPEALS (2ND DIVISION) AND PETRON CORPORATION, G.R. No.
207843. JULY 15, 2015)

Conformably with our ruling in BPI Leasing Corporation that the application of Section 244 of the
NIRC is an exercise of quasi-legislative or rule-making powers of the Secretary of Finance, and since
RR 2-2012 was issued by the Secretary of Finance based on Section 244 of the NIRC, such
administrative issuance is therefore quasi-legislative in nature which is outside the scope of a
petition for certiorari. (CLARK INVESTORS AND LOCATORS ASSOCIATION, INC. vs. SECRETARY
OF FINANCE AND COMMISSIONER OF INTERNAL REVENUE, G.R. No. 200670. JULY 6, 2015)

In praying to restrain the collection of RPT, petitioner also implicitly questions the propriety of the
assessment of such RPT. This is because in ruling as to whether to restrain the collection, the RTC
must first necessarily rule on the propriety of the assessment. A certiorari petition questioning an
interlocutory order issued in a local tax case falls under the jurisdiction of the CTA. (CE CASECNAN
Page 50 of 53

WATER AND ENERGY COMPANY, INC. vs. THE PROVINCE OF NUEVA ECIJA, et al., G.R. No.
196278. JUNE 17, 2015)

Section 7 of R.A. No. 1125 as well as Section 3, Rule 4 of the Revised Rules of the Court of Tax Appeals
explicitly provide that the CTA has exclusive appellate jurisdiction over tax collection cases decided
by the RTC. (MITSUBISHI MOTORS PHILIPPINES CORPORATION vs. BUREAU OF CUSTOMS, G.R.
No. 209830, JUNE 17, 2015)

In case of an illegal assessment where the assessment was issued without authority, exhaustion of
administrative remedies is not necessary and the taxpayer may directly resort to judicial action. The
taxpayer shall file a complaint for injunction before the Regional Trial Court to enjoin the local
government unit from collecting real property taxes. The party unsatisfied with the decision of the
Regional Trial Court shall file an appeal, not a petition for certiorari, before the Court of Tax Appeals,
the complaint being a local tax case decided by the Regional Trial Court. The appeal shall be filed
within fifteen (15) days from notice of the trial courts decision. In this case, the petition for injunction
filed before the Regional Trial Court of Pasay was a local tax case originally decided by the trial court
in its original jurisdiction. Since the PEZA assailed a judgment, not an interlocutory order, of the
Regional Trial Court, the PEZAs proper remedy was an appeal to the Court of Tax Appeals. (CITY OF
LAPU-LAPU vs. PHILIPPINE ECONOMIC ZONE AUTHORITY; PROVINCE OF BATAAN,
REPRESENTED BY GOVERNOR ENRIQUE T. GARCIA, JR., AND EMERLINDA S. TALENTO, IN HER
CAPACITY AS PROVINCIAL TREASURER OF BATAAN vs. PHILIPPINE ECONOMIC ZONE
AUTHORITY, G.R. No. 184203, G.R. NO. 187583, NOVEMBER 26, 2014, J. LEONEN)

NAPOCOR filed a petition for declaratory relief based on the assessments of real property taxes the
Municipality of Navotas imposed. It then questioned the legality of the tax imposition. On appeal, the
CTA En Banc ruled that the RTC has jurisdiction over the case even though administrative remedies
were not exhausted. The Court clarified that although there are instances were resort to judicial
action is allowed, it is not so in the case at hand. The fact that a separate chapter is devoted to the
treatment of real property taxes, and a distinct appeal procedure is provided therefor does not justify
an inference that Section 7(a)(3) of R.A. 9282 pertains only to local taxes other than real property
taxes. Rather, the term "local taxes" in the aforementioned provision should be considered in its
general and comprehensive sense, which embraces real property tax assessments, in line with the
precept Generalia verba sunt generaliter inteligenciawhat is generally spoken shall be generally
understood. Based on the foregoing, the general meaning of "local taxes" should be adopted in
relation to Paragraph (a)(3) of Section 7 of R.A. 9282, which necessarily includes real property taxes.
In fine, if a taxpayer is not satisfied with the decision of the CBAA or the RTC, as the case may be, the
taxpayer may file, within thirty (30) days from receipt of the assailed decision, a petition for review
with the CTA pursuant to Section 7(a) of R.A. 9282. In cases where the question involves the amount
of the tax or the correctness thereof, the appeal will be pursuant to Section 7(a)(5) of R.A. 9282. When
the appeal comes from a judicial remedy which questions the authority of the local government to
impose the tax, Section 7(a)(3) of R.A. 9282 applies. Thereafter, such decision, ruling or resolution
may be further reviewed by the CTA En Banc pursuant to Section 2, Rule 4 of the Revised Rules of the
CTA. (NATIONAL POWER CORPORATION vs. MUNICIPAL GOVERNMENT OF NAVOTAS,
SANGGUNIANG BAYAN OF NAVOTAS AND MANUEL T. ENRIQUEZ, G.R. No. 192300, NOVEMBER
24, 2014, J. PERALTA)

Page 51 of 53

Philamlife sold its shares through a public bidding. However, the selling price was below the book
value of the shares. Hence, the BIR imposed donors tax on the price difference. Philamlife appealed
to the Secretary of Finance. Due to the adverse ruling, Philamlife appealed with the CA. CA alleged
that it does not have jurisdiction for jurisdiction lies with the CTA. The Court ruled that, the CTA can
now rule not only on the propriety of an assessment or tax treatment of a certain transaction, but
also on the validity of the revenue regulation or revenue memorandum circular on which the said
assessment is based. (THE PHILIPPINE AMERICAN LIFE AND GENERAL INSURANCE COMPANY
vs. SECRETARY OF FINANCE and COMMISSIONER OF INTERNAL REVENUE, G.R. No. 210987,
NOVEMBER 24, 2014, J. VELASCO, JR.)

The respondents allege that the Court of Tax Appeals has no jurisdiction to make an assessment in
cases of an administrative claim for tax refunds. The Supreme Court ruled that in an action for the
refund of taxes allegedly erroneously paid, the Court of Tax Appeals may determine whether there
are taxes that should have been paid in lieu of the taxes paid. Determining the proper category of tax
that should have been paid is not an assessment. It is incidental to determining whether there should
be a refund. (SMI-ED PHILIPPINES TECHNOLOGY, INC. vs. COMMISSIONER OF INTERNAL
REVENUE, G.R. No. 175410, NOVEMBER 12, 2014, J. LEONEN)

The Commissioner of Customs contends that the CTA should not take cognizance of the case because
of the lapse of the 30-day period within which to appeal, arguing that on November 25, 1998 URC
had already received the BoCs final assessment demanding payment of the amount due within 10
days, but filed the petition only on July 30, 1999. The Court ruled against the Commissioner of
Customs. The reckoning date was on date that the Commissioner of Customs denied the protest of
Oilink, July 12, 1999. The Commissioner of Customs posits that only when the ensuing decision of the
Collector and then the adverse decision of the Commissioner of Customs would it be proper for Oilink
to seek judicial relief from the CTA. The Court ruled that the principle of non-exhaustion of
administrative remedies was not an iron-clad rule because there were instances in which the
immediate resort to judicial action was proper. As the records indicate, the Commissioner of Customs
already decided to deny the protest by Oilink and stressed then that the demand to pay was final. In
that instance, the exhaustion of administrative remedies would have been an exercise in futility
because it was already the Commissioner of Customs demanding the payment of the deficiency taxes
and duties. (COMMISSIONER OF CUSTOMS vs. OILINK INTERNATIONAL CORPORATION, G.R. No.
161759, JULY 2, 2014, J. BERSAMIN)

UPDATED BY PALS & ATENEO DE DAVAO UNIVERSITY
FOR THE 2017 BAR OPERATIONS
By:
4th year Law: Alona Suzell Ruyeras
Hisham Nazz Biruar
Maria Ayra Batacan
Manuel P. Quibod Dean College of Law

Page 52 of 53

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