The USS Dewey sailed within 12 miles (20 kilometers) of Mischief Reef, in the Spratly Island chain, on Wednesday, in a "freedom of navigation operation," according to a US official.
China's Defense Ministry said Thursday two Chinese frigates had "warned and dispelled" the USS Dewey after had entered its waters "without permission."
"We firmly opposed to the US behavior of showing force and boosting regional militarization, and have made solemn representation to the US side," Defense Ministry spokesman Ren Guoqiang said.
While he didn't confirm details of this particular operation, Pentagon Spokesperson Capt. Jeff Davis told CNN, "We operate in the Asia-Pacific region on a daily basis, including in the South China Sea."
"We operate in accordance with international law. We fly, sail, and operate wherever international law allows," he added.
A crucial shipping route, China claims ownership of the vast majority of the South China Sea,
including the Paracel and Spratly island chains, a claim disputed by numerous other countries including the Philippines and Vietnam.
The Chinese government has reclaimed land and built up artificial islands in the sea, including on Mischief Reef, and deployed military assets to them
The US regularly undertook freedom of navigation operations in the South China Sea under former US President Barack Obama, but there had been suggestions the Trump administration was putting them off to avoid antagonizing China
. Analysts said that Wednesday's operation didn't necessarily indicate US policy in the South China Sea had changed.
"Sooner or later there had to be a freedom of navigation operation and here it is. Does that mean the US has changed its policy in the South China Sea? No. It's just a continuation of the Obama policy," Ian Storey, a senior fellow at the ISEAS Yusof Ishak Institute in Singapore, said.
The Pentagon says freedom of navigation operations are "not about any one country, or any one body of water."
Earlier operations request denied
Earlier in the year, the US military had requested permission to perform a freedom of navigation operation but it was turned down by the Pentagon, as part of an effort to ease US China relations
, a US defense official told CNN.
Capt. Davis had told CNN in early May that all future freedom of navigation operations would not be widely advertised as they had been under the Obama Administration. Instead, they would only be released publicly in an annual report.
The US has traditionally taken no position on the territorial disputes in the South China Sea but has repeatedly asserted its right to freedom of navigation in the disputed waters, with the US military flying and sailing its assets close to the islands China controls.
China says both the Paracels and the Spratlys are an "integral part" of its territory, offering up maps that date back to the early 20th century.
The US Navy's new actions in the South China Sea took place as Chinese President Xi Jinping praised his country's navy at the 12th Party congress of the People's Liberation Army, according to state media.
In his speech to the meeting, Xi commended the navy's work and said he wanted to build them into a strong and modern force.
The Chinese navy launched their first homegrown aircraft carrier in April,
the second in their fleet, as part of their efforts to build a "blue-water navy" able to operate anywhere in the world.
Does China have upper hand?
China has appeared in recent months to be gaining the upper hand in the long-running South China Sea dispute.
On Friday May 19, China and the Philippines held their first direct talks over the region, a move analysts said strengthened the Beijing's position.
Under Philippines President Rodrigo Duterte, who came to power in June 2016, there has been a greater focus on co-operating with China rather than confronting them over their claims.
"The Philippines under Duterte decided that we had to address the overdependence on one major power, whose capital is thousands of miles away and to pay attention to our neighborhood, particularly, to the biggest neighbor we have -- that is China," Philippine Ambassador to China Chito Santa Romana told CNN last week.
The incoming US administration initially took a more muscular approach toward the South China Sea, with Secretary of State Rex Tillerson comparing China's island building to Russia's taking of Crimea at his confirmation hearing. However, the White House later appeared to ease up on Beijing as it sought China's help in reining in North Korea.
But Storey said claims of victory on China's behalf were premature. "None of the central drivers have changed, which means that sooner or later tensions are going to ramp up again over some incident at sea or in the air," he said.