The foreign ministry said it has sent two notes of protest over the January 29 incident off Scarborough Shoal as well as the removal of critically endangered giant clams by Chinese fishermen in the area a week earlier.
A Chinese foreign ministry spokesman disputed Manila's version of the first incident today, stressing its coast guard was performing its "normal" duties on Chinese territory.
"The Philippines continues to urge China to respect the Philippines' sovereign rights and jurisdiction over Bajo de Masinloc," Foreign Secretary Albert del Rosario told AFP on Thursday, referring to the shoal by its local name.
The ministry alleged three Filipino-flagged vessels were "intentionally rammed" by a vessel with Chinese coastguard markings, causing damage and endangering the crews' lives.
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It also alleged 24 Chinese boats harvested endangered giant clams in the area a week earlier.
"The Huangyan island is an inherent part of Chinese territory," Chinese foreign ministry spokesman Hong Lei said today, calling the shoal by its Chinese name.
"The thing is, on January 29, multiple Philippine fishing boats lingered illegally in the shallow waters of the Huangyan island, disobeying the instruction of the Chinese side" to leave the area.
"The Chinese side urged the Philippine side to enhance supervision and education of its own fishermen to prevent similar incidents from happening again."
Hong did not address the other Philippine protest over the harvesting of giant clams on around the shoal.
China claims most of the South China Sea, a vital sea lane and fishing ground that is believed to hold vast mineral resources.
But the Philippines, Vietnam, Brunei and Taiwan also have overlapping claims over the waters, making the area a potential flashpoint.