A statement on the Defence Ministry's website said the Arleigh Burke class guided-missile destroyer USS Higgins and Ticonderoga class guided-missile cruiser USS Antietam entered waters China claims in the Paracel island group "without the permission of the Chinese government".
In a statement, ministry spokesman Wu Qian said Chinese navy vessels were deployed "to conduct legal identification and verification of the U.S. warships and warn them off".
China has controlled the Paracels entirely since violently seizing Vietnam's holdings in the area in 1974.
Chiefs from the Pentagon have continuously accused China of building up it military power in the South China Sea to gain control of oil and gas rich region.
The objective of their sail-by was a speck of land called "Woody Island", where China has developed airstrips and port facilities in recent years as part of a broader strategy of establishing bases in these islands to demonstrate and exercise its political claims.
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The U.S. warships were carrying out "freedom of navigation" operations, also called FONOPS, which the Navy says are a means to challenge excessive maritime claims and uphold rights to use of the sea under global law.
The missions were hailed by state media as a major step in boosting the combat capabilities of the Liaoning, which was bought as a mostly empty hull from Ukraine and commissioned in 2012 along with its flight wing.
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters. China's behavior is inconsistent with the principles and purposes of the RIMPAC exercise'.
The U.S. Department of Defense cited China's moves to militarize the Spratly Islands, where it has constructed seven artificial islands, as a reason for the disinvitation. It called on China to remove these systems.
American warships will continue to be deployed in the region "on an everyday basis", Pentagon spokesman Lt. Col. Christopher Logan told the Russian media on Sunday.
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