The two sides are trying to hammer out a deal before the March 1 deadline when US tariffs on $200 billion worth of Chinese imports are scheduled to increase to 25 percent from 10 percent. The ships entered the waters without China's permission, ministry spokeswoman Hua Chunying told reporters.The US warships sailed near the islands the same day that China resumed trade talks with Washington.
The spokesperson also demanded the US stop what she called its "provocative actions", adding her country will take necessary actions to protect state sovereignty.
Tensions between US President Donald Trump and China's leader Xi Jinping have escalated in recent months, costing both countries billions of dollars.
She urged the U.S. to cease the "provocative actions".
The FONOP involved the Arleigh Burke-class guided-missile destroyers USS Spruance and USS Preble, which patrolled through the area to "challenge excessive maritime claims and preserve access to the waterways as governed by global law", as U.S. Navy 7th Fleet spokesman Cmdr.More news: NASA plans sustainable missions to make people stay on the Moon
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The Spratly Islands are a disputed group of islands, islets and cays and more than 100 reefs, sometimes grouped in submerged old atolls, in the South China Sea. The deployment is seen as the latest attempt by Washington to stand up to what it believes are attempts by Beijing to limit freedom of navigation in the strategic waters, where Chinese, Japanese and other Southeast Asian navies operate. In January, the destroyer USS McCampbell challenged China's claims to the Paracel Islands.
Beijing and Washington remain at loggerheads over USA allegations for China's militarisation of the South China Sea by building military installations on artificial islands and reefs.
China says the construction is necessary for defence, and it was the U.S. that was responsible for tensions by sending warships and military planes close to islands Beijing claims.
It was the second such USA operation in the South China Sea this year.
Top US officials have attacked China for everything from human rights abuses to cyber espionage in America.
Brunei, Indonesia, Malaysia, the Philippines, Taiwan, and Vietnam also have territorial claims in the region.