The foreign ministry issued a statement expressing "resolute opposition" to the US sail-by of the territory in the disputed Paracel Island chain on Sunday.
The US military conducts what it calls "freedom of navigation" voyages in the South China Sea to contest Beijing's assertion of territorial rights in the area, although the US has no claims of its own in the disputed region.
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The US Navy's Higgins and Antietam warships, a destroyer and cruiser respectively, entered China's territorial waters without permission and were met by the Chinese Navy, which "conducted verification and identification of US ships according to law and warned them to leave," the ministry said.
State-run news agency Xinhua said the two vessels were 'expelled' from the waters.
The operation was conducted just over a week after Beijing flew nuclear-capable bombers to a disputed island in a bold powerplay to show its military might and boost its territorial claims in the area.
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The move prompted immediate criticism from the US, which last week pulled its invitation to China to join maritime exercises in the Pacific because of Beijing's "continued militarisation" of the South China Sea.
Beijing has been building artificial islands to reinforce its claim over most of the resource-rich South China Sea despite protests from Southeast Asian countries.
Its neighbours, particularly some of those involved in maritime disputes over the waters, have expressed fears China could eventually restrict freedom of navigation and overflight.
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