Valdes was chief of staff of the Armed Forces of the Commonwealth of the Philippines from 1939, and was in 1941 appointed Secretary of National Defense by President Manuel L. Quezon.

[5][3][1][2][6] With the growing threat of Japanese expansion during the 1930s, President Manuel L. Quezon established the Department of National Defense in November 1939, which had executive authority over the army.

[6][1][3] As a member of the War Cabinet, he was tasked by General Douglas MacArthur to be in charge of the safety of President Quezon, who was very ill by that time, and his family.

Later the same month, the Commonwealth of the Philippines was reestablished and President Osmeña appointed Valdes as ad interim Secretary of Public Health and Welfare, officially taking the position on June 27, 1945.

[5][2][6] Valdes, along with the future Secretary of Foreign Affairs Raul Manglapus, at the time a reporter for the Philippines Free Press, were the only two Filipinos accredited to join MacArthur during the signing of the Instrument of Surrender on board the USS Missouri in Tokyo Bay on September 2, 1945.

[7] Valdes received one of 20 original facsimiles of the Instrument of Surrender, being one of eight personal guests of MacArthur, and his document is currently owned and curated by The International Museum of World War II in Natick, Massachusetts.

[8] In January 1946 Valdes was appointed as one of the judges at the Military Tribunal of Japanese General Masaharu Homma in view of the war crimes committed by his command during the invasion of the Philippines, sitting on the bench along with Leo Donovan, Robert G. Gard, Arthur Trudeau, and Warren H.