Japan, the Philippines and the United States were cooperating to protect the freedom of the South China Sea as they are committed to helping enhance Manila's security capabilities.
Japanese Prime Minister Fumio Kishida said on Saturday.
"In the South China Sea, trilateral cooperation to protect the freedom of the sea is underway," Kishida, on an official visit, said in an address before the Philippine Congress in the capital, Manila.
Kishida and President Ferdinand Marcos Jr agreed on Friday to start negotiations on a reciprocal troop access deal to strengthen military cooperation as China becomes increasingly assertive in the region.
The Philippines and Japan, two of the United States' closest Asian allies, have taken a strong line against what they see as aggressive behaviour by Chinese vessels amid decades-old disputes over maritime sovereignty.
China claims sovereignty over almost the entire South China Sea, including parts of the exclusive economic zones of Brunei, Indonesia, Malaysia, the Philippines and Vietnam. The Permanent Court of Arbitration in 2016 said China's claims had no legal basis.
"Japan will continue to contribute to the enhancement of the Philippines' security capabilities, thereby contributing to regional peace and stability," Kishida said.
Japan in March observed U.S.-Philippine military drills, and in June, the Philippine and Japanese coast guards trained together for the first time.
"Through these efforts, let us protect the maritime order, which is governed by laws and rules, not by force," said Kishida, who in December unveiled Japan's biggest military build-up as it looks to counter China's growing military might.
Japan has no claim to the South China Sea but has a maritime dispute with China in the East China Sea.
Kishida said Japan agreed to provide the Philippines coastal surveillance radars, the first cooperation project in the world under its Official Security Assistance programme, aimed at helping boost the deterrence capabilities of Tokyo's partner countries.
"Japan intends to further deepen strategic cooperation with the Philippines in the future," said Kishida, who is to make a stop at the Philippine Coast Guard on Saturday before leaving Manila.
Kishida said his country's relationship with the Philippines had reached a "golden age."
Last month, China and the Philippines traded accusations over a collision in the disputed waters of the South China Sea as Chinese vessels blocked Philippine boats supplying forces there.