Marcos' trip comes a week after Manila announced a deal giving US troops access to another four bases in the country, and with Japan and the Philippines already in talks on a key defence pact.
The so-called Reciprocal Access Agreement (RAA) would allow the countries 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 pacts with Britain and Australia.
Marcos and Japanese Prime Minister Fumio Kishida are not expected to complete negotiations on the RAA deal immediately, but they will likely agree to measures aimed at speeding up military deployments for humanitarian assistance and disaster relief.
The two leaders are taking an incremental approach towards the RAA, probably to avoid provoking Beijing, Renato DeCastro, distinguished professor in the International Studies Department at De La Salle University in Manila, told AFP.
"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 said.
In Beijing's view, "this might the beginning of an Asian NATO. Because you really have Asian countries strengthening and enhancing their security partnerships."
Before departing on Wednesday, Marcos called his trip to Japan an "essential" part of a drive to strengthen partnerships "with major countries in the region amid a challenging global environment".
He said he was "actively seeking" collaborations with Tokyo in areas including "agriculture, renewable energy, digital transformation, infrastructure, defence and security".
He and Kishida are expected to sign seven agreements covering those areas on a trip that will also see Marcos meet Japan's emperor on Thursday afternoon.
Worried about Beijing's growing assertiveness on Taiwan and bases in the disputed South China Sea, Manilla has been repairing ties with Washington that were fractured in recent years.
Given its proximity to Taiwan and its 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.
Japan is the Philippines' biggest diplomatic source of active development assistance, according to Manila, and its second-largest trading partner.
It is also the only country to have a bilateral free trade agreement with the Philippines.
Kishida is expected to affirm several loan agreements and extensions for Philippine infrastructure projects, including a $3 billion exchange of notes to finance major commuter rail projects.
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