Citing U.S. officials speaking on condition of anonymity, the newswire said USS John S. McCain sailed close to Mischief Reef in the Spratly Islands, an area which China is in a territorial dispute over with its neighbors.
Geng said the Chinese navy "identified the U.S. warship, warned and expelled it".
It was not immediately clear if the Chinese demanded the USA destroyer leave as they have done in the past.
"China is very displeased with this and will bring up the issue with the U.S. side", the ministry added. "The Chinese military is firmly opposed to such flaunting of force and promotion of militarization in the region by the US, which could easily trigger accidents at sea and in the air". USA officials say the military will continue to sail, fly and operate wherever permitted by global law.
Pentagon spokesman Lieutenant Colonel Chris Logan declined to comment on whether there had been a freedom of navigation sailing, but said: "We are continuing regular Fonops, as we have routinely done in the past and will continue to do in the future". "Summaries of these operations will be released publicly in the annual FONOPS report, and not sooner".
But the United States has snubbed that claim by sailing ships through the huge waterway. 12 nautical miles from shore marks the territorial boundary for all nations.More news: ASX in a $20b sell down as global tensions mount
The patrol was the third under Trump, and the second this year around Mischief Reef, a land feature that was included in a ruling last year against China by an worldwide arbitration court in The Hague.
China claims almost all of the South China Sea, despite partial counter-claims from Taiwan and several south-east Asian nations including the Philippines, Brunei, Malaysia and Vietnam. Beijing called the move a "serious political and military provocation". About 45 islands are occupied by relatively small numbers of military forces from China, Malaysia, the Philippines, Taiwan and Vietnam.
The Center for Strategic and International Studies' Asia Maritime Transparency Initiative (AMTI) wrote in an analysis just after November's US presidential election that the FONOP location most directly related to enforcement of the arbitration court ruling was Mischief Reef, which was found to be a low-tide elevation that does not generate an entitlement to a territorial sea, exclusive economic zone or continental shelf.
China considered this a large concession to the USA, the Guardian said.