Foreign Department spokesman Charles Jose announced the protest a day after the airing of a television interview in which President Benigno Aquino raised the alarm over the Chinese vessels at Reed Bank.
"The frequent passage of Chinese vessels in Recto Bank is not an innocent exercise of freedom of navigation but is actually done as part of a pattern of illegitimate sovereign patrol in the Philippines' exclusive economic zone, pursuant to China's unilateral effort to change the status quo in the South China Sea," Jose told reporters, referring to Reed Bank by its Filipino name.
In contrast, Jose said the bank was 595 nautical miles from the coast of China's Hainan island.
A day earlier, Aquino expressed concern at the presence of Chinese government ships in the disputed waters, questioning how far China intended to push its claims.
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In an interview with ABC-5 television network, transcripts of which were released by the presidential palace, Aquino said: "They want to claim what is ours. How far will we let this go? Are we going to be content to just tell them, 'Okay, you can go this far'"?
Defence Department spokesman Peter Paul Galvez said today the ships were "hydrological research vessels" capable of mapping the ocean floor, adding they were first sighted in June but could remain at sea for over a month.
China lays claim to almost all of the South China Sea, even up to the coasts of its neighbors. This conflicts with the territorial claims of the Philippines as well as Brunei, Malaysia, Taiwan and Vietnam.
In recent years, tensions between the Philippines and China have risen as China has aggressively pressed its claim, citing "historical facts" and occupying and fortifying outcrops and islets.
Aquino's spokesman Herminio Coloma said today the Philippines would continue to rely mainly on a "strategy of finding a peaceful and diplomatic solution" to the South China Sea dispute.