Japanese Occupation (1941-1945): There are no recorded or documented cases of executions

through the death penalty during this period simply because extrajudicial executions were widely
practised as part of the pacification of the country.

http://factsanddetails.com/southeast-asia/Philippines/sub5_6f/entry-3913.html

d) Japanese period (1941-1944)

The invasion of the Japanese forces when Clark Field, an American military airbase in Pampanga, was
bombed on December 8, 1941, marked the start of the Japanese period which lasted for three years. A
Japanese Republic was established with Jose P. Laurel as its President. Jose Yulo was the Chief Justice of
the Supreme Court. This period was considered as a military rule by the Japanese Imperial Army. The
1943 Constitution was ratified by a special national convention of the Kapisanan sa Paglilingkod ng
Bagong Pilipinas (KALIBAPI). This period lasted for three years and ended in 1944 with the defeat of the
Japanese forces.

https://www.nyulawglobal.org/globalex/Philippines.html

World War II and the Third Republic

During World War II, the National Assembly passed legislation granting emergency
powers to President Manuel L. Quezon; Chief Justice Jose Abad Santos was made
concurrent Secretary of Justice and acting President of the Philippines in unoccupied
areas. After his capture and execution at the hands of the Japanese, the Commonwealth
government-in-exile had no system of courts.

Meanwhile, the Japanese organized the Philippine Executive Commission in occupied

areas on January 8, 1942, which gave way to the Second Republic in October 14, 1943.
By the end of World War II, the regular function of the courts had been restored, beginning
with the appointment of a new Supreme Court on June 6, 1945. On September 17, 1945,
the laws of the Second Republic were declared null and void; a Supreme Court decision
on Co Kim Cham v. Eusebio Valdez Tan Keh and Arsenio P. Dizon recognized this.

https://www.officialgazette.gov.ph/about/gov/judiciary/

UNDERSTANDING THE SECOND PHILIPPINE REPUBLIC

The Second Philippine Republic was established during the Japanese occupation of the
Philippines. At the outset of the occupation, the Japanese government established a
military administration over the Philippines, as well as the Philippine Executive
Commission, composed of several pre-war Filipino political leaders. The KALIBAPI
(Kapisanan ng Paglilingkod sa Bagong Pilipinas) was also organized, designed to be the
sole and exclusive political organization in the Philippines.
On June 16, 1943, Premier Hideki Tojo promised independence to the Philippines. The
KALIBAPI would then form the Preparatory Committee on Philippine Independence
(PCPI), which was tasked with drafting a new Constitution. The new Constitution
was approved by the Preparatory Committee on Philippine Independence on September
4, 1943 and ratified by the KALIBAPI on September 7, 1943.

The KALIBAPI then proceeded to elect part of the new National Assembly, which also
included appointed members; in turn, the National Assembly elected its Speaker and then
elected Jose P. Laurel as President. On October 14, 1943, in ceremonies in front of the
Legislative Building in Manila, the new Republic was inaugurated, and Jose P. Laurel, the
Chairman of the Preparatory Committee, assumed office as President.

On September 21, 1944, President Laurel proclaimed martial law in the Philippines (it
came into effect on September 22). On September 23, 1944, Laurel proclaimed that the
Philippines was “in a state of war” with the Allied Powers—but this was never ratified by
the National Assembly. In large part, Japanese dissapointment with Laurel led to the
Republic under Laurel being superseded by the Makapili, organized in December, 1944
to more militantly oppose the returning American forces and Filipino guerrillas. The
Japanese brought the Laurel government to Baguio in December, 1944, and a small
remnant of that government was taken to Tokyo in March, 1945. Laurel formally dissolved
the Second Republic on August 17, 1945, two days after Japan surrendered to the Allies.

When the Commonwealth government was restored on Philippine soil on October 23,
1944, Field Marshal Douglas MacArthur as military commander had issued a
proclamation nullifying all acts of the Philippine Executive Commission and the Second
Republic. The Supreme Court of the Philippines reiterated this nullification in a decision
(G.R. No. L-5) on September 17, 1945 (and subsequent decisions), but pointed out
President Osmeña recognized the validity of some judicial acts of a non-political nature.
The Supreme Court categorized the Philippine Executive Commission and the Second
Republic as a de facto (actual, whether by right or not) government, in contrast to the de
jure (meaning rightful, or legitimate) status of the Commonwealth government. While
this means no laws or regulations from the Second Republic are legally recognized,
President Laurel has been included in the roster of Philippine presidents since the 1960s.

Many officials who served in the Philippine Executive Commission, the Second Republic
and its various agencies were charged with treason but received an amnesty from
President Manuel Roxas on January 28, 1948.

http://malacanang.gov.ph/5235-70th-anniversary-of-the-second-philippine-republic/