[2] At the time, the embassy's six staff members, including both Vargas and León María Guerrero III, who served as its second secretary, made up the Second Republic's entire foreign service.

[1] Although the embassy had been in operation for two years, the pre-war Commonwealth of the Philippines never recognized its establishment, and it was summarily closed with Japan's defeat in World War II.

[6] In 1956, after Japan and the Philippines signed agreements addressing wartime reparations, thereby normalizing relations between the two countries,[7] Congress would pass Republic Act No.

The villa — highly acclaimed at the time — featured an observatory tower and was surrounded by Japanese gardens with tall trees and laced with imported stones.

[11] In 1976, the embassy relocated to a three-story building on a 2,490-square-meter (26,800 sq ft) site in Nanpeidaichō, which was also turned over to the Philippine government as part of Japan's war reparations.

Ramos led a groundbreaking of the project on November 19, 1997 while transiting through Tokyo on his way to APEC Canada 1997 in Vancouver, and construction of the 2,413-square-meter (25,970 sq ft) building was completed in February 2003.

[16] The Philippine government has, on a number of occasions, contemplated either disposing of or redeveloping the properties in its Japanese portfolio, generating significant controversy in the process.

Disposal of the Roppongi, Nanpeidaichō and other Japanese properties, including that of the Kudan, have also been contemplated during the presidencies of Gloria Macapagal Arroyo,[19] which opted instead to redevelop them,[20] and Rodrigo Duterte.

In 2019, Jose Antonio Sy-Alvarado, who represents the first district of Bulacan in the House of Representatives, filed a bill which would have authorized the sale of the properties to fund the pensions of Filipino war veterans; this elicited strong opposition from Foreign Affairs Secretary Teodoro Locsin Jr.,[18] who also criticized attempts to sell the properties to fund the Philippine government's response to the COVID-19 pandemic,[14] and was joined in this regard by Senators Franklin Drilon and Leila de Lima.

[34] A number of prominent Filipinos have also served as ambassadors to Japan, including Jose S. Laurel III, son of former President José P. Laurel, former Foreign Affairs Secretary Domingo Siazon (who notably served as Ambassador twice), businessman Alfonso Yuchengco, and Roberto Benedicto, a crony of former President Ferdinand Marcos, father of Bongbong Marcos.