Manila has been holding the naval drills with its longtime ally Washington since 1995. But the exercise with Tokyo, a World War II foe, is only its second ever after one earlier this year.
This week's Cooperation Afloat Readiness and Training (CARAT) drill with Washington will include a P-3 Orion aircraft, of the type used by the US to monitor the South China Sea.
China claims almost the entire Sea despite competing claims from the Philippines, Brunei, Malaysia, Taiwan and Vietnam, and has been taking strong action including reclamation to assert sovereignty.
Rear Admiral Leopoldo Alano, commander of the Philippine Fleet, described the drill as a great opportunity "to gain valuable experience and increase our inter-operability."
The drills will also feature for the first time the littoral combat ship USS Fort Worth, and involve the rescue and salvage ship USNS Safeguard.
While it does not take sides in the dispute, the US has in recent weeks intensified its criticism of China's reclamation work, which has created new islands including airstrips on reefs and shoals also claimed by its neighbours.
China said last week its land reclamation in the disputed Spratly islands would finish soon but be followed by "facility construction".
The Philippines has asked a United Nations tribunal to reject China's claims to most of the Sea, a move angrily rejected by Beijing which says the world body has no authority in the matter.
This week's naval exercise will be held both on Palawan, the closest land mass to the disputed reefs and waters, and in the Sulu Sea to the east of the island.
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