China has slammed the US for sailing a warship near disputed territory in the South China Sea, saying the move was a "serious illegal act" and "deliberately provocative".

In a statement on its website late Friday night, the country's defence ministry said two Chinese naval vessels warned off a US ship after it entered "Chinese territorial waters" near the Paracel Islands, known as Xisha in Chinese.

China controls all of the islands, which are also claimed by Vietnam and Taiwan.

The ship's "entrance into China's territorial waters is a serious illegal act and a deliberately provocative act," it said, adding that the ministry had made "solemn representations" to Washington.

In a separate online statement, the foreign ministry said the action had "seriously violated China's sovereignty and security interests, and had seriously broken relevant Chinese law and international law."

The Pentagon said Friday it had sent the destroyer USS Decatur close to the Paracel Islands, but that the ship had not passed within the 12 nautical mile zone that international law defines as territorial waters.

The ships transited the area in "a routine, lawful manner without ship escorts and without incident," a spokesman said.

The manoeuvre was the third South China Sea "freedom of navigation" operation conducted this year by the US, which has repeatedly stressed it will ignore China's "excessive" maritime claims.

Friday's operation was the first since a tribunal at the Permanent Court of Arbitration in The Hague in July ruled there was no legal basis to China's claims to nearly all of the sea -- a verdict Beijing dismissed vehemently.

China that month held a week of military drills around the Paracels in the northern part of the South China Sea, during which other ships were prohibited from entering the waters.

Several other nations across the region including the Philippines and Vietnam have rival claims to various parts of the South China Sea.

The US action came as Philippine President Rodrigo Duterte wrapped up a four-day state visit to China, where he pledged to increase cooperation with Beijing, while at the same time slamming his country's long-time ally Washington.

In a joint statement at the end of his trip, the Chinese and Philippine leaders pledged to resume talks over their own territorial dispute in the South China Sea.