Beijing claims virtually the entire South China Sea, and has built up a series of man-made outposts in what the Asia Maritime Transparency Initiative at the Center for Strategic and International Studies (CSIS) think tank has said is a bid to create "fully functioning air and naval bases".
It said two Chinese Navy ships "took immediate action to identify and verify the U.S. ship, and warned and dispelled it".
"We conduct routine and regular freedom of navigation operations, as we have done in the past and will continue to do in the future", said Lieutenant Commander Nicole Schwegman, a spokeswoman for U.S. Pacific Fleet.
Neither the Chinese Ministry of Foreign Affairs nor the Chinese Ministry of National Defense immediately responded to a request for comment.
In its own statement late Friday, China's defense ministry said two Chinese Navy ships "took immediate action to identify and verify the USA ship, and warned and dispelled it".
"By repeatedly sending military ships into these areas without authorisation, the United States has seriously harmed Chinese sovereignty and security, violated basic rules of worldwide relations, and harmed regional peace and stability".
The other nations which have conflicts with China regarding territory in the South China Sea are Brunei, Malaysia, Taiwan, Vietnam and the Philippines.More news: Osaka cruises past Kasatkina to claim maiden title — WTA Indian Wells
According to U.S. official, this move was to counter Beijing's strategy of limiting navigation in the strategic waters like the South China Sea.
"The Chinese military is firmly opposed to it", the Chinese Ministry of Defence added.
The United States has criticized China's construction of islands and build-up of military facilities in the sea, and is concerned they could be used to restrict free nautical movement. "(We are) firmly opposed to such flaunting of force and promotion of militarization in the region by the U.S., which could easily trigger accidents at sea and in the air", it said in a statement at the time. "It is not aimed at any specific country or target", the newspaper reported.
For many years the South China Sea has been considered an global flashpoint, as the USA and China attempt to assert their influence in the region.
The operation carried out by the USS Mustin will likely draw attention to its timing because it comes a day after the Trump administration proposed $60 billion in trade tariffs on China.
The announcement came after Taiwan's Defense Ministry said Wednesday that it had dispatched jets and ships to shadow a Chinese aircraft carrier group that sailed through the Taiwan Strait in a southwesterly direction, apparently into the South China Sea.