Japanese Foreign Minister Takeshi Iwaya met with his Filipino counterpart Enrique Manalo and with Philippine President Ferdinand Marcos in Manila to affirm security commitments.
Iwaya and Manalo discussed Beijing's efforts to assert control over the South China Sea, a strategic trade route, as well as Beijing's territorial and sovereign rights claims in the East China Sea that overlap with Japan's.
"In response to the developments in the South China Sea, we agreed to further strengthen Japan-Philippines partnership," Iwaya told a joint news conference.
He vowed continuing Japanese assistance to enhance the "maritime security" and "maritime safety capabilities" of the Philippines, which has been engaged in increasingly tense confrontations with China over disputed South China Sea waters and reefs in the past year.
China claims most of the strategic waterway despite an international tribunal ruling that its claim lacked any legal basis.
Manila expressed concern this week over Chinese coast guard ships patrolling close to its coast.
Iwaya told reporters "I am gravely concerned that actions heightening tension in the South China Sea are repeated".
This was a "legitimate concern for the international community because it directly links to regional peace and stability", he added.
Manalo said "our geopolitical security environment is growing more and more complex and challenging" and expressed concern over "unilateral actions that aim to undermine the rule of law in the East and South China Seas".
"So we agreed to work together in that context, not only to address issues in the sense of defence and security, but to enhance resilience and enhance adaptive... capacity of our nations."
Japan is a key financer of Philippine efforts to modernise its South China Sea patrol craft as well as maritime surveillance systems.
Iwaya said he and Manalo also agreed to strengthen their trilateral partnership with the United States.
They pledged to "maintain good communication with the next US administration, to maintain and strengthen the momentum for our trilateral cooperation", Iwaya added.
The United States has a decades-old security alliance with the Philippines that includes a mutual defence treaty and a 2014 pact which allows the US military to store equipment on nine Philippine bases.
In a telephone call with US Vice President Kamala Harris on Wednesday, Marcos "expressed optimism in maintaining the strong and dynamic relationship" between the two allies under the incoming Trump administration.
Trump, who will be sworn in as president on Monday, has pushed an "America First" agenda based on avoiding foreign conflicts and protectionist trade policies.
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