The Philippines summoned China's ambassador on Monday to explain what it called the "illegal intrusion and lingering presence" of a Chinese navy vessel in waters between some of the archipelago nation's largest islands.
The foreign ministry in a statement said a Chinese navy reconnaissance ship entered Philippine waters without permission and lingered from Jan. 29 to Feb. 1, ignoring repeated demands to leave.
It was detected off the Cuyo Group of Islands, close to Palawan, and Apo island off Mindoro, a presence the ministry said "did not constitute innocent passage and violated Philippine sovereignty".
China has been accused by Western countries of aggression by deploying hundreds of coast guard and fishing vessels in the exclusive economic zones of its neighbours and disrupting fisheries and energy exploration work, far off its mainland.
The deployment of military vessels in waters to which China has no claims is rare, however. China's embassy in Manila did not immediately respond to a request for comment.
The Philippines foreign ministry did not say why it waited six weeks to report the incident. The defence minister did not immediately respond to a request for comment.
Despite efforts to build closer ties with China, the Philippines has become more critical of its actions, including what it calls "swarming" by fishing vessels manned by militias off the disputed Spratly islands, and its blockade of a military resupply mission.
The last time a Chinese ambassador was summoned was in April last year.
China's foreign minister Wang Yi in January said Beijing would not use its strength to "bully" its smaller neighbours.
(Reporting by Karen Lema; Editing by Martin Petty)