The USS Preble was one of two warships conducting the operation; they were shadowed by Chinese assets, but the interactions were routine and uneventful, according to a USA official.
Washington has hit back in the past, claiming it is countering Beijing's militarisation of the South China Sea by building army installations on artificial reefs and islands.
Beijing and Washington are locked in a trade war and the two sides are trying to hammer out a deal ahead of a March 1 deadline when United States tariffs on $200 billion worth of Chinese imports are scheduled to increase to 25 per cent from 10 per cent.
A U.S. official said the warships had approached the islands on Monday to counter Chinese claims of domination over the entire South China Sea.
It was the second such United States operation in the South China Sea this year.
Cmdr. Clay Doss, U.S. Seventh Fleet public affairs officer, told Fox News in a statement: "Guided-missile destroyers USS Spruance (DDG 111) and USS Preble (DDG 88) conducted freedom of navigation operations (FONOPS) in the South China Sea". A spokeswoman for the Chinese foreign ministry, Hua Chunying, accused the USA of entering Chinese waters without permission and engaging in provocations that threaten China's sovereignty, the South China Morning Post reported.
China illegally asserts control over the disputed Spratlys and surrounding waters.
A spokesman for the 7th Fleet said the mission was conducted "in order to challenge excessive maritime claims and preserve access to the waterways as governed by global law". In January, the destroyer USS McCampbell sailed within 12 nautical miles of the Paracel Islands. The official said Monday's operation focused on Mischief Reef, a location claimed by China, Vietnam and the Philippines.
Doss added: "We conduct routine and regular Freedom of Navigation Operations (FONOPS), as we have done in the past and will continue to in the future".
'The relevant actions of the United States warships violated Chinese sovereignty, and undermined peace, security, and order in the relevant sea areas, ' Hua said.
China says the construction is necessary for defence, and it was the USA that was responsible for tensions by sending warships and military planes close to islands Beijing claims.
During a South China Sea freedom-of-navigation operation in September, a Chinese destroyer challenged a US vessel to a showdown, forcing the US Navy ship off course and risking a deadly collision.