Speaking as he concluded a two-day visit that included a tour of Philippine air bases, Japanese defence secretary Gen Nakatani said the two countries hoped to achieve greater operational collaboration in the future.
"Secretary (Gilberto) Teodoro Jr and I firmly concurred that the security environment surrounding us is becoming increasingly severe and it is ... necessary to further enhance defence cooperation," Nakatani said.
He added the countries had agreed to establish "strategic dialogue between high-level operational officers".
Nakatani's visit comes on the heels of a January foreign ministers' meeting where the Philippines and Japan vowed to strengthen security cooperation to counter China's actions in key sea trade routes, including the disputed South China Sea.
Philippine defence chief Teodoro Jr. told Monday's joint press briefing the two countries shared the "common cause of resisting any unilateral attempt to reshape ...international law by force".
China has deployed navy and coast guard vessels in a bid to bar the Philippines from strategically important reefs and islands in the South China Sea, leading to a string of confrontations in recent months.
In December, the Philippines said the Chinese coast guard used water cannon and "sideswiped" a government fisheries department vessel.
And last week, the Philippine coast guard said a Chinese Navy helicopter came "within 10 feet" (three metres) of a surveillance plane carrying journalists over the contested Scarborough Shoal.
Japan is a key financier of Philippine efforts to modernise its South China Sea patrol craft as well as maritime surveillance systems including radar installations.
Beijing claims the strategic waterway in almost its entirety despite an international tribunal ruling that its claim lacked any legal basis.
Japan has its own ongoing dispute with China over uninhabited islands in the East China Sea -- known as the Diaoyu in China and Senkaku in Japan -- which are claimed by Beijing but administered by Tokyo.
Both Tokyo and Manila are longtime allies of the United States, which has been strengthening an arc of alliances to deter China's claims in the Pacific.
Late last year, the Philippine Senate ratified a key pact with Japan that would allow them to deploy troops on each other's soil.
The agreement, which now awaits ratification in Tokyo, also allows for increased joint combat drills.
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