The Philippines accused China on Thursday of ramming Filipino fishing boats off a disputed shoal in the South China Sea, and demanded its powerful neighbour respect its sovereignty over the potential flashpoint territory.

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 on Thursday, 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.

China must "desist from undertaking activities that not only imperil the lives, safety and livelihood of Filipino fishermen but also damage the fragile marine environment in that area", del Rosario added.

The ministry alleged three Filipino-flagged vessels were "intentionally rammed" by a vessel with Chinese coastguard markings, causing damage and endangering the crews' lives.

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 Thursday, 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.

A coast guard dinghy was sent to relay the order, "and some of the boats bumped slightly into each other", said Hong.

"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.

China has controlled the Scarborough Shoal, a rich fishing ground in the South China Sea 220 kilometres (137 miles) west of the main Philippine island of Luzon, since 2012 following a tense standoff between the Filipino navy and Chinese maritime patrol vessels.

The shoal is 650 kilometres from Hainan island, the nearest major Chinese land mass.

In February 2014, the Philippines filed a protest accusing Chinese coastguard of using water cannon to drive off Filipino fishermen near the shoal.

The Philippines has also accused China of conducting "massive" reclamation work in the Spratlys, a group of reefs and islands also located in the South China Sea, including atop reefs claimed by Manila.

Manila has asked a United Nations arbitration panel to rule on its maritime disputes with Beijing.

"China intends to seize as much of the South China Sea as possible," Michael Tkacik, a security specialist with the Texas-based Stephen F. Austin State University, told a security forum in Manila on Wednesday.

Sparring over islands, shoals and outcrops might drag China into conflict with another superpower, the United States, a traditional military ally of the Philippines, he warned.