The Foreign Ministry confirmed on Thursday that the Coast Guard drove off Philippine fishing boats that had illegally entered Chinese waters off Huangyan Island last month and had refused requests to leave.
A Philippine vessel had "a slight scratch", the Ministry said.
Earlier on Thursday, the Philippine Department of Foreign Affairs issued a statement accusing Chinese Coast Guard vessels of "deliberately ramming" three Philippine fishing boats on Jan 29.
Foreign Ministry spokesman Hong Lei told a media conference in Beijing that, "on Jan 29, several Philippine fishing boats were illegally positioned in the shoal waters off Huangyan Island," and they refused to respond to requests to leave.
The China Coast Guard ships then drove them off in accordance with the law, and one of the Philippine boats had "a slight scratch", Hong said.
"Huangyan Island is part of China's inherent territory. The Chinese government vessels fulfill their duties in the waters off Huangyan Island and maintain order in the waters in accordance with the law," Hong said.
China urged the Philippines to improve oversight of its fishermen and make sure such incidents never happen again, Hong said.
Manila's claims to the island has led to tension in the China-Philippine relationship. A serious standoff took place in waters off the island in April, 2012.