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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.
"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.
Arleigh Burke-class guided-missile destroyer USS Dewey in the South China Sea on May 5.
"Sooner or later there had to be a freedom of navigation operation and here it is. Does that mean the US has changed it's 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."
A satellite image of Mischief Reef showing military installations.
Earlier operations request denied
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.
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.
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.
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.
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.