
The deal signing by officials from both sides was broadcast by Philippines state media.
It was part of seven agreements struck during an official visit by President Ferdinand Marcos Jr to Tokyo, state media said.
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 US 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 US greater access to military bases in the Philippines.