The USS Dewey destroyer sailed less than 12 nautical miles from a reef claimed by Beijing, which warned the US risked disrupting negotiations between stakeholders in the South China Sea.
The Chinese government charged on Thursday that a US warship had entered its waters in the South China Sea "without permission", prompting China's navy to warn the vessel to leave.
China warned that the United States risked severely disrupting negotiations between stakeholders in the South China Sea.
"The relevant action taken by the US vessel undermines China's sovereignty and security interests," foreign ministry spokesman Lu Kang told a press briefing after the USS Dewey destroyer sailed less than 12 nautical miles from a reef claimed by Beijing on Thursday morning.
Kang said China urged the US to correct its mistake and refrain from further patrols, adding such actions were very likely to cause unexpected air and sea accidents.
US officials, speaking on condition of anonymity, confirmed the USS Dewey passed close to the Mischief Reef in the Spratly Islands, among a string of islets, reefs, and shoals over which China has territorial disputes with its neighbours.
"Freedom of navigation"
This was the first "freedom of navigation" exercise under President Donald Trump, a US official said.
In a statement, the US Department of Defense stressed that its Freedom of Navigation Operations programme performs exercises that are "not about any one country, nor are they about making political statements."
What makes South China Sea a disputed area?
It is a territorial dispute over a busy waterway. Goods worth $5.3 trillion pass through the South China Sea, which is also rich in marine life, contributing to 10 percent of the world's fish trade.
Natural resources are also abundant here. The US Energy Information Agency estimates there are some 11 billion barrels of oil and 190 trillion cubic feet of natural gas reserves under the sea, exceeding what some of the world's biggest energy exporters have.
Who claims the disputed waterways?
The main countries are the ones geographically close to the disputed waterway. China, Brunei, Malaysia, the Philippines, Taiwan, and Vietnam all have overlapping claims to the South China Sea. China claims almost the entire stretch.
The US regards the South China Sea as international waters and wants it to be "free" for navigation under the UN maritime law.
What is the Exclusive Economic Zone?
The United Nations Convention on the Law of the Sea (UNCLOS) says that states can control the territorial waters within 200 nautical miles (370 km) off their shores. These are called the Exclusive Economic Zones (EEZ).
The convention passed in 1982 states that areas that do not fall under EEZ should be international waters, shared by everyone and free for navigation.
However, China asserts it is entitled to more than the 200 nautical miles from its shores.
In 1947, China outlined its claim to the disputed waterway by drawing a map with a U-shaped line covering almost 70 percent of the South China Sea.
Referred to as the nine-dash line, it covered the Paracel and Spratly islands, and a cluster of more than 30 others.
It has rapidly built reefs into artificial islands capable of hosting military planes.
The US has challenged annexations of these islets and advocated for a diplomatic settlement of the disputes.
According to the Pentagon, the US in 2016 conducted operations "challenging excessive maritime claims of 22 coastal states, including allies and partners."