The US slammed China for its "escalation" in the key global shipping route where Beijing is accused of deploying warships, arming outposts and ramming fishing vessels. Most recently, Vietnam voiced concerns on China's movements near Spratly Islands.
USS Carl Vinson's arrival marks biggest US military presence since 1975 and comes at a time China seeks to expand influence in South China Sea.
The USS Stethem destroyer passed less than 12 nautical miles (22 kilometres) from tiny Triton Island in the Paracel Islands archipelago, which is also claimed by Taiwan and Vietnam, according to a US defense department official.
The assertion of Philippine sovereignty over the islands in the South China Sea signifies an apparent change of tack likely to anger China.
More than half-a-dozen countries have been drawn into an argument over the control of a waterway that serves as an important trade route and is rich in natural resources.
The Pentagon report comes at a time of heightened tension over maritime territories claimed by China and disputed by several Asian nations.
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