Chinese coast guard vessels on Sunday drove away two Filipino ships, carrying supplies to Filipino soldiers stationed on a warship on Second Thomas Shoal.
The shoal is called Ayungin Shoal by Manila and Ren'ai Reef by the Chinese.
"The Foreign Ministry has summoned the head of the Philippines embassy in China to lodge solemn representation on this event," Foreign Ministry spokesman Qin Gang said at a daily briefing.
The Philippine Department of Foreign Affairs protested against China's interference and said the actions "constitute a clear and urgent threat to the rights and interests of the Philippines" under the Law of the Sea.
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The Filipino troops awaiting fresh supplies are stationed on the warship that ran aground on the beach of the Ren'ai Reef in 1999. The Philippines claimed the ship had been stranded.
China urged the Philippine side to stop provocations, honour its words, pull away its ship from the reef and to implement the Declaration on the Conduct of Parties in the South China Sea, Qin said.