"We conduct routine and regular Freedom of Navigation Operations (FONOPs), as we have done in the past and will continue to do in the future", U.S. Pacific Fleet said in a statement.
The U.S. Defense Department refused to confirm the operation took place.
The US military did not directly comment on Sunday's operation, but said US forces operate in the region daily.
It said the Chinese military "immediately dispatched warships to identify and inspect the American ships according to law, and warned them to depart".
It has also built seven man-made islets in the Spratlys, with three - Fiery Cross, Subi and Mischief reefs - all boasting military-grade airfields, despite a 2015 pledge by Chinese President Xi Jinping not to further militarize them.
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Called "Xisha" in Chinese, the islands have been incorporated into the southern province of Hainan and are being developed for tourism, as well as being equipped with weapon systems meant to enforce China's claim to virtually the entire South China Sea. The island has hosted multi-role fighters, surface-to-air missiles, and anti-ship cruise missiles.
The Vietnamese government protested China's move as a violation of its sovereign claim to the islands-exactly the language used by China to protest United States actions today after sending its own warships to warn away the Americans. Clay Doss, told the Times that similar operations have been conducted in 22 countries.
Critics of the operations, known as a "freedom of navigation", have said that they have little impact on Chinese behaviour and are largely symbolic. "Sticking to the "status quo" with just one warship to do (the) FONOP could no longer be seen as a tenable situation since obviously the previous approach doesn't work in reining in Chinese behavior".
Beijing has slammed the move as a "provocation" and an infringement of China's sovereignty.
"(Beijing) said some red lines, we said some red lines.
The dispute in the South China Sea has strained not only the relations between China and its neighbors, but has also made companies and countries very careful in exploring for oil resources in the area.