China's People's Liberation Army said the US ship had "illegally" entered waters near the reef without Chinese approval, and its forces had monitored the vessel and warned it.
United States Navy destroyer sailed near one of the most important man-made and Chinese controlled islands in the South China Sea on Monday, in a freedom of navigation mission that Beijing denounced as illegal.
While the United States frequently makes such voyages to challenge China and other states' territorial claims in the strategic waterway, the latest one took place as Beijing staged more war games around Taiwan.
The US Navy's 7th Fleet said the USS Milius had engaged in "normal operations" within 12 nautical miles of Mischief Reef in the Spratly Islands, once a reef submerged at high tide and where China has built an airport and other facilities.
"Under customary international law [...] features like Mischief Reef that are submerged at high tide in their naturally formed state are not entitled to a territorial sea," the 7th Fleet said in a statement.
"The land reclamation efforts, installations and structures built on Mischief Reef do not change this characterization under international law."
China's People's Liberation Army said the US ship had "illegally" entered waters near the reef without Chinese approval, and its forces had monitored the vessel and warned it.
"China has indisputable sovereignty over the islands in the South China Sea and the surrounding maritime area," its Southern Theater Command said.
Mischief Reef lies to the west of the Philippines' Palawan island.
The 7th Fleet said at the end of the operation, the Milius exited the "excessive claim area" and continued operations in the South China Sea.
Last month, China and the US sparred over the movement of the same ship, which China said had entered its territorial waters in the South China Sea near the Paracel Islands.
China claims vast swathes of the area through which trillions of dollars in trade flow every year.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam also claim all or parts of the South China Sea.
Philippines’ military bases
Separately, Philippine President Ferdinand Marcos Jr assured China on Monday that military bases accessible to the US would not be used in any offensive action, stressing the arrangement with Washington was designed to boost his country's defenses.
China's foreign ministry last week said the US strengthening military deployment in the Philippines would only lead to more tension in the region, after Manila allowed Washington access to more of its bases.
"China's reaction was not surprising," Marcos told reporters. "The Philippines will not allow the bases to be used in any offensive action," he said.
The Philippines identified last week four more of its bases the US will get access to, almost doubling the number included in its Enhanced Defense Cooperation Agreement (EDCA).
The locations of the bases are significant, with three facing north toward Taiwan and one near the disputed Spratly Islands in the South China Sea, where China has built artificial islands equipped with runways and missile systems.
EDCA underlines the Philippines' strategic importance to the former colonial ruler the US, coming at a time of growing concern over China's conduct in the South China Sea and tension over Taiwan.
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