MANILA (AFP) - 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.

"The Philippines continues to urge China to respect the Philippines' sovereign rights and jurisdiction over Bajo de Masinloc," Foreign Affairs 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", Mr del Rosario added.

The ministry alleged three Filipino-flagged vessels were "intentionally rammed" by a vessel with Chinese coast guard markings, causing damage and endangering the crews' lives. It also alleged 24 Chinese boats harvested endangered giant clams in the area a week earlier.

Later on Thursday, Beijing defended the actions of the coast guard vessel and urged Manila to increase "indoctrination" of its fishermen.

"China's coast guard sent a dinghy to drive them away and slightly bumped one of the fishing vessels," Chinese Foreign Ministry spokesman Hong Lei said at a daily news briefing. "We ask that the Philippines strengthen education and indoctrination of its fishermen to prevent such incidents from happening again."

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 west of the main Philippine island of Luzon, since 2012 following a tense standoff between the Filipino navy and Chinese maritime patrol vessels.

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.