The destroyer USS Stethem passed less than 12 nautical miles (22 kilometres) from tiny Triton Island in the Paracel Islands archipelago, which is also claimed by Taiwan and Vietnam, the official told AFP.
USA forces regularly dispatch warships to carry out "freedom of navigation patrols" in the tense region.
China did not immediately issue a response.
Sunday's operation will may draw extra scrutiny given a series of other actions taken by the Trump administration in recent days that may be suggestive of a change in approach by the United States to the U.S.
On Thursday, the administration imposed sanctions on two Chinese citizens and a shipping company for helping North Korea's nuclear and missile programs, and accused a Chinese bank of laundering money for Pyongyang.
"China is altering physical and political landscapes by creating and militarizing man-made bases", Harris said.
Despite largely praising Chinese president Xi Jinping, President Trump has also mounted pressure on Beijing to do more to sway North Korea to halt its nuclear programs and attempted missile launches.
But when those efforts failed to produce results - Pyongyang conducted new missile tests in violation of UN Security Council resolutions - the American president made his frustration known.
The United States has routinely conducted voyages within this 12-mile limit around islands in the South China Sea as a message to countries such as China, Taiwan, Vietnam and the Philippines. The global standard is that territorial waters extend 12 miles from a shoreline.
In the Paracel Island chain and in the Spratlys, China has built up a number of small islands into fully functional military facilities complete with airfields and antiaircraft defenses.
The updated report (available in this link) could raise tension anew among nations with overlapping claims on the strategic waterway, including the Philippines, which recently sent its top diplomat to China at the latter's "invitation" as both countries endeavor to rebuild ties that had been tested by their maritime dispute.
The Xisha Islands are an inherent part of the Chinese territory, Lu said, noting that in accordance with the Law of the People's Republic of China on the Territorial Sea and the Contiguous Zone, the Chinese government promulgated the baseline of the territorial sea off the Xisha Islands in 1996.
The first came on May 24, when the guided-missile destroyer USS Dewey sailed within 12 miles (20 kilometers) of Mischief Reef in the Spratly Islands chain, which lies to the south of the Paracels.
New satellite imagery released last week by the Center for Strategic and International Studies' Asia Maritime Transparency Initiative indicates that China is continuing to build military facilities in the Spratly Islands.