Prime Minister Yoshihiko Noda and Philippines President Benigno Aquino III agreed Tuesday in Tokyo to forge closer maritime security ties to resolve disputes with China in the South China Sea.
China and the Philippines have experienced heightened tensions over the Spratly Islands, which are believed to lie on top of vast oil deposits. They are also claimed by Vietnam, Taiwan, Malaysia and Brunei.
Tokyo and Beijing are engaged in a territorial row of their own over the Senkaku Islands in the East China Sea.
Tuesday's agreement could irk China.
"The two leaders confirmed that the South China Sea is vital, as it connects the world and the Asia-Pacific region, and that peace and stability therein is of common interest to the international community," read a joint statement released by Noda and Aquino.
Aquino has been in Japan since Sunday for a working visit, traveling to disaster-hit Ishinomaki, Miyagi Prefecture, on Monday while also taking time to meet with Japanese business executives in an effort to gain fresh investments.
Japan is the Philippines' top trade partner and largest donor. The joint statement underlined the importance of the joint economic partnership agreement between the two nations that went into effect in 2008.
On Wednesday, Aquino will visit Emperor Akihito, who will host a state luncheon for the president at the Imperial Palace before he heads back to the Philippines.