"Chinese military took immediate actions by dispatching naval ships and aircrafts to conduct legal identification and verification of the USA warships and warn them off", Wu Qian, defense ministry spokesman, said.
The ministry said late Sunday that the Chinese military had warned the two USA warships to leave after they entered waters near the contested Paracel Islands in the strategic waterway.
The US military did not directly comment on Sunday's operation, but said US forces operate in the region daily.
While this operation had been planned months in advance, and similar operations have become routine, it comes at a particularly sensitive time and just days after the Pentagon uninvited China from a major US-hosted multinational naval drill.
Critics of the operations have said that they have little impact on Chinese behavior and are largely symbolic, but Collin Koh, a specialist in regional naval affairs at Singapore's S. Rajaratnam School of International Studies, said Sunday's patrol appeared different.
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China's claims in the South China Sea, through which about $5 trillion in shipborne trade passes each year, are contested by Brunei, Malaysia, the Philippines, Taiwan and Vietnam. Earlier in the month, the United States also formally protested the deployment of missiles and radar equipment on three artificial islands China has built in the Spratly Islands.
The Paracel islands are part of a territorial dispute that China has with neighbouring countries.
The Philippines has notified China of its "red lines"-potential Chinese actions that would be unacceptable to Manila-in the South China Sea, including oil and gas extraction in disputed areas, the Philippine Foreign Secretary Alan Peter Cayetano said on Monday".
It also follows the United States' decision to disinvite the Chinese People's Liberation Army-Navy from the 2018 iteration of the Rim of the Pacific exercise. China's behavior is inconsistent with the principles and purposes of the RIMPAC exercise'.
Trump's cancellation of a summit with North Korean leader Kim Jong Un has put further strain on U.S.
Chinese officials have accused Washington of viewing their country in suspicious, "Cold War" terms.