She urged the United States to cease the "provocative actions".
Trade talks between the USA and China have resumed and China is reportedly upbeat.
According to reports, the USS Spruance and USS Preble, both guided-missile destroyers, sailed within 22 km of the Spratly Island chain.
The operation was carried out "to challenge excessive maritime claims and preserve access to the waterways as governed by worldwide law", Cmdr.
Analysts have said it would be hard for the world's two largest economies to resolve their trade disputes by the designated date, given the challenge of U.S. demands for structural reform in China to address issues of intellectual property protection, forced technology transfers and state subsidies favouring domestic companies.
Freedom of navigation operations, or FONOPS, are meant to remind other countries that all nations can operate in global waters. Other regional nations-such as the Philippines and Vietnam-lay claim to part of the waterway and the US routinely pushes back against China by sending ships to patrol the sea.
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.
It comes at a time of increasing tensions between the United States and China over an ongoing trade war.
Observers fear the trade dispute is just one element in the deteriorating relationship between the world's two top economies with top White House officials sharply criticising Beijing for everything from human rights abuses to cyber-warfare.
The United States is expected to keep pressing China on longstanding demands that it reform how it treats American companies' intellectual property in order to seal a trade deal that could prevent tariffs from rising on Chinese imports.
In mid-January, US and British warships conducted their first joint military exercises in the South China Sea since Beijing began building bases and air strips on islands.
The two countries are also at loggerheads over regional security, with the USA offering support to the island nation of Taiwan, which China also claims as its own.
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