China's Foreign Ministry said in a statement that the vessel "illegally entered into the waters of China's Spratly Islands."
"The action taken by the US warship has threatened China's sovereignty and security interest, and has put the safety of personnel on the reefs in danger," the ministry said.
A US defense official told CNN that the destroyer USS Lassen "conducted a transit" within 12 nautical miles of Subi Reef in the Spratly Islands on Tuesday morning local time.
The operation put the ship within an area that would be considered Chinese sovereign territory if the US recognized the islands as being Chinese territory, the official added.
The United States hadn't breached the 12-mile limit since China began massive dredging operations to turn three reefs into artificial islands in 2014 -- even though maritime law doesn't usually accord territorial waters to islands built on previously submerged reefs.
China's Foreign Ministry reiterated that its activity in the South China Sea didn't affect freedom of navigation by sea or air but said it held "indisputable sovereignty over the Spratly Islands and its nearby waters."
"China is resolutely opposed to any country damaging China's sovereignty and security interest in the name of freedom of navigation and overflight," it said.