Speaking on condition of anonymity, U.S. officials have revealed the ship carried out the "freedom of navigation operation" within 12 nautical miles of the artificial island.
China's foreign ministry said the operation had "violated worldwide and Chinese law and seriously harmed Beijing's sovereignty and security".
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 operation occurred at an awkward and tense moment in the region, amid the war of words between the United States and North Korea.
The US، however، says it supports none of the territorial claims and only sends the warships to protect what it calls "freedom of navigation" in the South China Sea، which acts as a strategic transfer route for Chinese goods and is believed to be rich in natural resources.
However, the USA officials said that the USS John S. McCain sailed past an island in the disputed Spratly chain in the South China Sea, which is the third mission under the Trump administration. That occurred around Triton Island in the Paracel archipelago, which is claimed by China, Vietnam and Taiwan.
"Such a move severely undermines China's sovereignty and security, and severely endangers the safety of frontline personnel of both sides", he said.More news: Gorka denies dismissing Tillerson's role on North Korea
Beijing upbraided the United States for the Thursday's operation - the third reported under the Trump administration. The Chinese Foreign Ministry issued a similar statement.
The CSIS report said 64 per cent of China's maritime trade passed through the sea, compared to 14 per cent of USA maritime trade.
Although China opposes inclusion of the sea disputes in worldwide conferences, partly to prevent the U.S. and other Western governments from intervening, U.S. Secretary of State Rex Tillerson, Australian Foreign Minister Julie Bishop and Japan's new top diplomat, Taro Kono, expressed concern over aggressive actions in the waters.
The US 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.
The Philippines on Friday stressed that it has not received reports of China's recent land reclamation activities in the South China Sea prior to the ASEAN Ministerial Meeting (AMM) in Manila. "It is clear who is not willing to see stability in the South China Sea and who is the major factor pushing for militarization in the South China Sea".
On the other hand, China stressed that all its activities in this area are carried out in accordance with the global law and that Japan is not in a stance to interfere.
The Joint Communiqué reflects the consensus of the ministers on issues concerning ASEAN, wherein Vietnam and the Philippines are member states.