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 buffeting our region," Marcos said following talks with Japanese Prime Minister Fumio Kishida.
Japan is "one of the Philippines' closest neighbours and closest friends", Marcos told reporters.
His trip comes a week after the Philippines announced a deal giving US troops access to another four bases in the country.
Tokyo and Manila are also in preliminary discussions over a key defence pact that would allow them to deploy troops on each others' 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.
But for now, the leaders are taking an incremental approach to defence cooperation, probably to avoid provoking Beijing, said Renato DeCastro, distinguished professor in the International Studies department at De La Salle University in Manila.
"Both countries are still very much aware that they have touched a sensitive nerve in China (by) creating the possibility of an Asian encirclement of China," DeCastro told AFP.
In Beijing's view, "this might be the beginning of an Asian NATO. Because you really have Asian countries strengthening and enhancing their security partnerships."
Worried about Beijing's growing assertiveness on Taiwan and bases in the disputed South China Sea, Manila has been repairing ties with Washington that were fractured in recent years.
Given its proximity to Taiwan and surrounding waters, cooperation from the Philippines would be key in the event of a conflict with China.
Japan last year announced a major defence overhaul, pledging to double defence spending to the NATO standard of two percent of GDP by 2027 and designating China the "greatest strategic challenge ever" to its security.
Japanese PM Kishida said the countries would continue to review "cooperation regarding defence equipment, technology and strengthening cooperation between Japan, the US and the Philippines".
Japan is also the Philippines' biggest diplomatic source of active development assistance, according to Manila, and its second-largest trading partner.
It is the only country to have a bilateral free trade agreement with the Philippines.
On Thursday, the countries also agreed loan agreements and extensions for Philippine infrastructure projects, including $3 billion to finance major commuter rail projects.
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