The USS Lassen warship began its mission through waters near the disputed Spratly archipelago at about 6.40am local time on Tuesday.
“The operation has begun … It will be complete within a few hours,” a senior US defence official was quoted as saying by Reuters.
Chinese officials were not informed of Tuesday’s mission, US officials said.
As reports of the “freedom of navigation” operation emerged, China’s foreign minister, Wang Yi, warned Washington to “act prudently to avoid provocation”.
China’s official news agency, Xinhua, said Wang had urged the US to “think twice, and not act rashly and make trouble out of nothing”.
In a further statement, the foreign ministry in Beijing said: “China strongly urges the US side to conscientiously handle China’s serious representations, immediately correct its mistake and not take any dangerous or provocative acts that threaten China’s sovereignty and security interests.”
The Chinese embassy in Washington said the concept of freedom of navigation should not be used as an excuse for muscle flexing and the United States should “refrain from saying or doing anything provocative and act responsibly in maintaining regional peace and stability”.
But there was no immediate sign of a more robust military response from Beijing.
Ian Storey, a South China Sea expert at Singapore’s institute of Southeast Asian studies, said Washington’s decision to deploy a warship rather than a smaller vessel underlined its determination to issue a powerful signal of intent.
“They’ve gone in heavy. There is not much else heavier than that except an aircraft carrier,” he said. “They want to send a very clear message to China that they are serious about this.”
Rory Medcalf, the head of the National Security College at the Australian National University, said the operation was “a warning for China not to overplay its hand in signalling that America is not welcome in the South China Sea”.
Storey said the “$64,000 question” was how Beijing would respond to the long-anticipated US move, which follows months of escalating tensions in the region, where Beijing has overlapping territorial claims with countries including Vietnam and the Philippines.
“China will have to react – it cannot not react to this,” Storey said. “Nationalism in China is such that China will be expected to make a robust response to this.
“This is why the US has had to consider these operations very carefully,” he added. “They’d have to take into account how China would respond. And if China does move to challenge these operations using coastguard operations or naval ships then that raises the risk of a collision or worse.”
The Spratly islands in the South China Sea.
China’s military buildup in the South China Sea – including the construction of a 3km runway capable of supporting fighter jets and transport planes - has become a major source of tension between Beijing and Washington.
Subi and Mischief reefs were submerged at high tide before China began a massive dredging project in 2014. It now claims a 12-nautical-mile territorial limit around the artificial islands, although the UN Convention on the Law of the Sea says such limits cannot be set around man-made islands built on previously submerged reefs.
US president Barack Obama said he had held “candid discussions” with Chinese president Xi Jinping over the issue during Xi’s recent state visit to the US.
However, Medcalf said Tuesday’s operation, for which the navy had been preparing for months, indicated Washington was unsatisfied with the outcomes of those talks.
“Clearly there was a decision to wait until after the Xi Jinping visit and I suspect to base American behaviour on the outcomes of that visit,” he said.
Speaking earlier this month, officials in Beijing cautioned the US against “provocative” actions in the South China Sea. “China will never allow any country to violate China’s territorial waters and airspace in the South China Sea,” foreign ministry spokeswoman Hua Chunying said.
China claims most of the South China Sea, one of the world’s busiest sea lanes, although Vietnam, Malaysia, Brunei, the Philippines and Taiwan have rival claims. Beijing says the islands will have mainly civilian uses as well as undefined defence purposes.
But satellite photographs have shown the construction of three military-length airstrips by China in the Spratlys, including one each on Mischief and Subi reefs.
Pentagon officials have spent months lobbying for the White House to take a harder line on China’s actions in the South China Sea, which is a key global shipping lane, through which more than $5tn of world trade passes every year.
“There are billions of dollars of commerce that float through that region of the world,” White House spokesman Josh Earnest told a news briefing. “Ensuring that free flow of commerce … is critical to the global economy.”
Ashton Carter, the US defence secretary, has accused Beijing of constructing “massive outposts” in the South China Sea that increase “the risk of miscalculation or conflict” in the region.
“Make no mistake, we will fly, sail and operate wherever international law permits,” Carter said earlier this month. “We will do that in the time and place of our choosing.”
Pentagon officials said Tuesday’s mission, the first such operation since 2012, would be the first of many.
Earlier reports said the ship would likely be accompanied by a US navy P-8A surveillance plane and possibly P-3 surveillance plane, which have been conducting regular surveillance missions in the region.
“The United States’ credibility is at stake here,” said Storey. “If it just did a one-off symbolic drive-by then US credibility suffers in the region so this I think is going to be the first of many such operations in the future.”
Pentagon officials say the United States regularly conducts freedom-of-navigation operations around the world to challenge excessive maritime claims.
In early September, China sent naval vessels within 12 miles of the Aleutian Islands off Alaska. China said they were there as part of a routine drill following exercises with Russia.
Australian defence minister Marise Payne said her country had not been involved in Tuesday’s manoeuvres but indicated support for the US move.
“It is important to recognise that all states have a right under international law to freedom of navigation and freedom of overflight, including in the South China Sea. Australia strongly supports these rights,” Payne said in a statement.