A Chinese Foreign Ministry spokesman said in a statement that the USS John S. McCain had violated Chinese and global law, undermined Chinese sovereignty and security, and endangered the safety of frontline personnel.
"China is resolutely opposed to this kind of show of force and pushing of regional militarisation by the United States that may easily cause an unexpected incident at sea or in the air", it said.
In a statement late Thursday, Chinese Foreign Ministry spokesman Geng Shuang called the U.S. Navy's action a "provocation" that "severely undermines China's sovereignty and security, and severely endangers the safety of frontline personnel of both sides".
Tensions escalated a few years ago when China began to build seven reefs, including Mischief, into islands, including three with runways, which the USA and China's neighbors fear could be used to project Beijing's military might and potentially obstruct freedom of navigation.
Such operations, Nauert said, get the "most attention" when they occur in the South China Sea. The reef is an artificial island built by China in the Spratly Islands, known by China as the Nansha Islands.
China on Wednesday expressed strong dissatisfaction and firm opposition to Japan's defence white paper for 2017 which accused Beijing of trying to change the status quo in the East and South China Sea based on "its own assertions".
The US move came four days after the United States, Australia and Japan denounced Beijing's island-building and militarization of the South China Sea on the sidelines of a security forum of the 10-nation Association of Southeast Asian Nations (ASEAN) in Manila.
The ship entered the Meiji Reef in the disputed Spratly Islands on Thursday.
Defense Secretary Delfin Lorenzana acknowledged knowing of China's continuing improvement of structures on manmade islands in the South China Sea but said the government "will leave it at that".
The show of U.S. force came as the Trump administration upped the pressure on China to bring Pyongyang to heel, just hours after North Korea threatened to target a USA military base on the Pacific island of Guam.
"While there have been land reclamation activities that have taken place in the Paracels in the previous months based on the AMTI report, the same report did not indicate that such activity was taking place just prior to the ASEAN Ministerial Meeting (AMM)".
"Freedom of navigation is guaranteed and anyone can do it so we just need to monitor", Padilla said in the same Palace press briefing.
Twelve nautical miles marks the territorial limits recognised internationally.
Its sweeping claims overlap with Vietnam, the Philippines, Malaysia and Brunei - all ASEAN members - as well as Taiwan.
The U.S. military has a long-standing position that its operations are carried out throughout the world, including in areas claimed by allies, and they are separate from political considerations.