"The actions of the U.S. warship have threatened China's sovereignty and security interests, jeopardized the safety of personnel and facilities on the reefs, and damaged regional peace and stability," China's Foreign Ministry said in a statement on its website after the destroyer USS Lassen sailed close to the Subi Reef in the Spratly Islands.

The "U.S. side [should] think twice, not ... take rash moves and stir up troubles," China's Foreign Minister Wang Yi warned in a separate statement.

A U.S. defense official said the mission was part of an ongoing global effort to keep international waters open for navigation in the face of "excessive maritime claims." The official denied the U.S. was specifically targeting China.

China says virtually all of the South China Sea belongs to it. Beijing's claims over the group of at least a half dozen dredged islands, one of which includes a recently completed two-mile airstrip, have angered the Philippines, Vietnam, Malaysia, Brunei, and Taiwan, which have overlapping claims in the waters.

Related: China Builds Runway on Reef in Disputed Sea: Pentagon

The Spratlys sit in an area potentially rich in oil and gas reserves.

Along with other island chains in the South China Seas, Beijing claims the Spratlys as part of China's territory and argues that international law grants them a 12-mile exclusion zone. While the U.S. officially does not take sides in the dispute, it also does not recognize the exclusion zone.

"We have been clear that we take no position on competing territorial sovereignty claims to land features in the South China Sea," a Pentagon official told NBC News on Monday night.