The ministry said the Chinese military issued warnings to guided-missile cruiser USS Antietam and the USS Higgins to leave the waters after they "arbitrarily entered" the contested Paracel Islands in the waterway "without permission of the Chinese government".
Several US officials who declined to be named said the two US warships came within 12 nautical miles of the Paracel Islands, maneuvering near Tree, Lincoln, Triton and Woody islands in the operations.
The ministry said the course plotted by the vessels had "seriously infringed upon Chinese sovereignty" and "contravened Chinese and relevant worldwide law", as they had entered territorial waters without permission.
The operation was the latest attempt to counter what Washington sees as Beijing's efforts to limit freedom of navigation in the strategic waters.
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 Pentagon withdrew its invitation for China to participate in a multinational naval exercise the U.S.is hosting this summer, in what it called "an initial response" to China's militarization of the South China Sea.
These operations "are not about one country", he said, "nor are they about making political statements".
REUTERS An aerial view of Woody Island in the Paracels
FONOPS are regularly conducted in disputed seas throughout the world.
The move signals U.S. rejection of China's claims of political control in the South China Sea.
A US Navy soldier stands aboard the USS Higgins destroyer.
Satellite photographs taken on May 12 showed China appeared to have deployed truck-mounted surface-to-air missiles or anti-ship cruise missiles at Woody Island.
"China's continued militarization of disputed features in the South China Sea only serve to raise tensions and destabilize the region", a Pentagon spokesman, Marine Lt. Col. Christopher Logan, said.
China's military took "immediate action" on Sunday against "unauthorized" sailing by United States warships in South China Sea waters claimed by Beijing.
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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