Manila and Beijing are locked in a territorial dispute over the South China Sea, which Beijing claims almost its entirety, but the Philippines' foreign ministry said the Chinese vessel entered its archipelagic waters "without permission".

The Dongdiao-class electronic reconnaissance ship was in the Sulu Sea, the Philippines' largest waterway, from January 29 to February 1 and ignored repeated orders to leave.

The vessel claimed "it was exercising innocent passage" as it reached the Cuyo islands off Palawan and Apo island off Mindoro.

"Its movements, however did not follow a track that can be considered as continuous and expeditious, lingering in the Sulu Sea for three days," the foreign ministry said, accusing the vessel of an "illegal intrusion".

"The actions of PLAN 792 did not constitute innocent passage and violated Philippine sovereignty."

China's embassy in Manila did not immediately respond to a request for comment.

China claims almost all of the South China Sea, through which trillions of dollars in trade passes annually, with competing claims from Brunei, Malaysia, the Philippines, Taiwan and Vietnam.

Beijing has ignored a 2016 ruling by The Hague-based Permanent Court of Arbitration that its historical claim is without basis.

Tensions between Manila and Beijing flared up last year after hundreds of Chinese vessels were detected at Whitsun Reef in the Spratly Islands, which lie in the disputed waters.

In November, Chinese coastguard ships fired water cannon at Philippine boats delivering supplies to marines at Second Thomas Shoal, also in the Spratly Islands.