"The foreign ministry expresses its serious concern and firm opposition over the Philippines' dispatch of naval vessels to Renai (Second Thomas) Shoal in the Spratly Islands," it said in a statement.
Taiwan's government "denies all unlawful claims to sovereignty over, or occupation of, these areas by other countries" it said.
The statement did not say when and how many Philippine ships were allegedly sent to the area or for how long. A foreign ministry spokeswoman was not immediately available for comment when reached by AFP.
The potentially resource-rich sea, home to important trade routes, is an increasingly dangerous flashpoint and there have been a string of recent diplomatic rows between countries with overlapping territorial claims.
The Philippine government and military spokespeople declined to comment.
Taipei and Manila have already been embroiled in a diplomatic row over the fatal shooting of a Taiwanese fisherman by Philippine coastguards who claimed his vessel had intruded into their territorial waters earlier this month.
Taiwan has rejected claims that the shooting took place in Philippine waters and that the killing was "unintended". President Ma Ying-jeou has described the incident as "cold-blooded murder".
Taiwan has also recalled its de facto envoy and held a military exercise in waters near the northern Philippines last week.
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