The agreement, called a terms of reference, sets out how their armed forces would work together during disaster relief operations, the Philippines defence ministry said in a statement.
It was struck during an official visit by President Ferdinand Marcos Jr to Tokyo, his first since taking office in July.
Japanese officials previously told Reuters that the disaster relief deal would make it easier to establish a broader legal framework allowing Japanese forces to deploy to the Philippines.
Some lawmakers in the Philippines have called for the country to sign a so-called visiting forces agreement with Japan, which allows them to deploy forces on each other's soil. Tokyo recently signed such deals with Australia and Britain, and also hosts the biggest concentration of U.S. forces abroad.
Marcos, who said his visit to Japan was aimed at forging "stronger defence and security cooperation" among other matters, last week signed an agreement granting the United States greater access to military bases in the Philippines.
(Reporting by Sakura Murakami in Tokyo and Neil Jerome Morales in Manila; Editing by Raju Gopalakrishnan and Christina Fincher)
