The countries agreed on measures to speed up military deployments for humanitarian assistance and disaster relief.
They also signed several other deals, ranging from infrastructure loans to cooperation on agriculture and technology.
After our meeting, I can confidently say that our strategic partnership is stronger than ever as we navigate together the rough waters that buffet our region," Marcos said after talks with Japanese Prime Minister Fumio Kishida.
Marcos said that Japan is one of the Philippines' closest neighbours and closest friends.
His trip comes a week after the Philippines announced a deal that gives the United States troops access to four more bases in the country.
Tokyo and Manila are in preliminary discussions over a key defence pact that would allow them to deploy troops on each other's territory for training and other operations.
Japan, which invaded and occupied the Philippines during World War II, has recently inked similar deals with Britain and Australia.
Renato DeCastro, professor at De La Salle University, said that the leaders are taking an incremental approach to defence cooperation, probably to avoid provoking Beijing.
Both countries are aware that they have touched a sensitive nerve in China, as they have created the possibility of an Asian encirclement of China, DeCastro told AFP.
In Beijing's view, this could be the beginning of an Asian North Atlantic Treaty Organization, he said, because you really have Asian countries strengthening and strengthening their security partnerships.