Japanese and Philippine military planes flew together near disputed South China Sea waters on Tuesday, as the two countries deepened their alliance in the face of separate territorial disputes with China.

A Japanese P-3C Orion and a Philippine Islander plane flew together from the western island of Palawan with three Filipino military observers aboard the Japanese plane, according to Philippine spokesman Commander Lued Lincuna.

"They flew outside the territorial waters for a familiarisation flight. Outside, going west," he told AFP.

The Philippines and China are embroiled in a dispute over territory in the South China Sea.

However, Lincuna said the bilateral exercise was not connected to the tensions.

"We focus on non-traditional activities being conducted by the navy like search and rescue and human assistance and disaster relief," Lincuna said.

The flight took place on the second day of separate but simultaneous Philippine naval exercises with the United States and Japan.

The Philippines, which has one of the region's weakest militaries, has been expanding its defence ties with both the US and Japan, to get backing against China's claim.

Philippine Navy spokeswoman Lieutenant Liezl Vidallon said the exercises with the US "are not related to the disputed islands. These annual, bilateral exercises will continue with or without the territorial disputes."

Last month, China said it "drove away" a US P-8 Poseidon plane flying over one of the artificial islands it has created from reclaimed land to press its claims in the South China Sea.

On Tuesday it cautioned the Philippines, the United States and Japan against playing up the naval drills.

"As I've said lots of times, we hope that relevant countries will not hype up the tensions in the region and we also hope the relevant interactions will be conducive to the peace and stability of the region instead of the other way around," said foreign ministry spokesman Lu Kang in Beijing.

Aside from China and the Philippines, Vietnam, Brunei, Malaysia and Taiwan also have overlapping claims over the South China Sea.

The Philippines has challenged China's claims before a United Nations-backed arbitration body but Beijing has refused to take part in the proceedings.

Beijing is embroiled in a separate dispute with Tokyo over East China Sea islands.

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