"The US destroyer's behavior violated Chinese law and relevant international law, severely harmed China's sovereignty and security interests, and threatened the lives of both sides' frontline personnel," said Chinese Foreign Ministry spokeswoman Hua Chunying.
The remarks were made after the guided-missile destroyer USS Chafee sailed within 16 nautical miles of the disputed Paracel Islands.
She added that Beijing had lodged "stern representations" with Washington, while calling on the US to respect China's sovereignty.
Meanwhile, the Chinese Defense Ministry announced that the US' actions would affect trust between both countries' militaries and could trigger "unwanted incidents."
"In the face of repeated provocation by the US forces, the Chinese military will further strengthen preparation for combat at sea and in the air and improve the defenses to resolutely defend national sovereignty and security interests," said a statement released by the ministry.
It added that the Huangshan guided-missile frigate, two J-11B fighter jets and one Z-8 helicopter had been sent to deter the US ship from the region.
Earlier in the day, three US officials said the USS Chafee destroyer had sailed near the disputed Islands in the South China Sea in a so-called "freedom of navigation" operation.
The officials, speaking on condition of anonymity, told Reuters that the guided-missile destroyer had carried out normal maneuvering operations "very close" to the 12-nautical-mile territorial limits of the islands.
They further said the mission was undertaken to challenge "excessive maritime claims" near the Paracel Islands, over which China has territorial disputes with its neighbors.
The situation in the South China Sea has been precarious since Japan and South Korea, two major allies of the US in the region, protested what they described as China's undercutting of naval sovereignty of neighboring nations in the region.
The US, which routinely carries out military drills in the sea along with Japan and South Korea, has called on China to retract its military presence from waters, which are not part of its territory.
Washington claims that China has blocked free movement of vessels in areas, which should be used for international navigation without any restriction under the international protocol.
China, however, has objected to US intervention in the area, accusing Washington of seeking to destabilize the region and undermine the unity among the Southeast Asian nations.
The US does not make any claims in the sea, but has long been taking the side of China's rival claimants in the regional disputes, which involve Vietnam, Taiwan, the Philippines, Malaysia, and Brunei.