Foreign ministry spokesman Geng Shuang said the actions of the USS John S McCain had violated Chinese and international law, "seriously" impairing the country's sovereignty and security.
"China is strongly dissatisfied with this," Geng said in a statement, adding that Beijing would lodge an official protest with Washington.
The USS John S McCain destroyer sailed within six nautical miles of Mischief Reef -- an artificial island built by China -- yesterday as part of a "freedom of navigation" operation, a US official said.
Speaking on condition of anonymity, the US official told AFP a Chinese frigate sent radio warnings at least 10 times to the USS McCain.
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"They called and said 'please turn around, you are in our waters'," the official said. "We told them we are a US (ship) conducting routine operations in international waters."
The official said the interactions were all "safe and professional," with the operation lasting about six hours from start to finish, but Geng said such operations "seriously endanger lives".
The US move came four days after the United States, Australia and Japan denounced Beijing's island-building and militarisation of the South China Sea on the sidelines of a security forum of the 10-nation Association of Southeast Asian Nations (ASEAN) in Manila.
China claims nearly all of the sea, through which $5 trillion in annual shipping trade passes and which is believed to sit atop vast oil and gas deposits.
Its sweeping claims overlap with Vietnam, the Philippines, Malaysia and Brunei -- all ASEAN members -- as well as Taiwan.
On Sunday China scored a coup when ASEAN ministers issued a diluted statement on the dispute and agreed to its terms on talks at the Manila meeting.
China insists that a much-delayed code of conduct between it and ASEAN members over the disputed sea must not be legally binding, a demand to which Southeast Asian countries have so far acquiesced.
Chinese defence ministry spokesman Wu Qian said the situation in the South China Sea has "stabilised" due to the "joint efforts" of China and neighbouring countries but the US operation threatened "peace and stability in the region".
The operation also comes amid soaring tensions on the Korean peninsula over Pyongyang's missile programme, and as the United States seeks to push China into more assertively restraining North Korea.
Pentagon spokesman Lieutenant Colonel Chris Logan declined to comment on whether there had been a freedom of navigation sailing but he said the United States would continue to do such operations.
"All operations are conducted in accordance with international law and demonstrate that the United States will fly, sail, and operate wherever international law allows," he said.