U.S. officials, speaking on condition of anonymity, told the Reuters news agency that two military vessels came within 12 nautical miles (around 22km) of the disputed Paracel Islands, among a string of islets, reefs and shoals over which China has territorial disputes with its neighbours.
The ministry said the course plotted by the vessels had "seriously infringed upon Chinese sovereignty" and "contravened Chinese and relevant global law", as they had entered territorial waters without permission.
Chinese defence chiefs have said U.S. warships entered the waters and did not leave when warned by Beijing's warships and aircraft.
The foreign ministry issued a statement expressing "resolute opposition" to the U.S. sail-by of the territory in the disputed Paracel Island chain on Sunday.
Foreign Secretary Alan Peter Cayetano provided on Monday more details of what President Rodrigo Duterte's administration has been doing to defend the country's sovereignty in the disputed region amid criticism that it has been far too soft on China.
Washington has said it would like to see more global participation in its freedom of navigation operations in the South China Sea, through which about $5trn of ship-borne trade passes each year.More news: Rockets lose Game 7 to Warriors 101-92
Sunday's freedom-of-navigation exercise came just days after the United States disinvited China to the upcoming Rim of the Pacific drills, citing evidence of Beijing's continued militarization of the disputed islands.
Both are in the contested Spratly Islands in the South China Sea, which is being claimed by the Philippines, China, Vietnam, Taiwan, Malaysia, and Brunei.
Critics of the operations, known as a "freedom of navigation", have said that they have little impact on Chinese behavior and are largely symbolic.
Satellite photographs taken on May 12 showed China appeared to have deployed truck-mounted surface-to-air missiles or anti-ship cruise missiles at Woody Island.
The disinvitation was made in retaliation for China's deployment of its H-6K strategic bomber on Woody island on May 18. RIMPAC is the world's largest maritime military exercise and is held bi-annually in Hawaii, usually in June and July.
China's Foreign Affairs Minister Wang Yi said the USA decision to exclude it from RIMPAC was 'very non-constructive'.
China has accused Washington of viewing Beijing in "Cold War" terms.