After a 79-hour search covering 26,000 square kilometres, the US Navy has ended a three-day search for a sailor who is believed to have gone overboard during operations in the South China Sea.

A statement on Friday said that US, Japanese and Chinese navy vessels and aircraft combed an area of the South China Sea west of the Philippines.

The sailor, from the guided-missile destroyer USS Stethem, based in Yokosuka, Japan, was reported missing at 9am (local time) and assumed overboard on August 1.

The destroyer was conducting routine operations in international waters west of the Subic Bay in the Philippines, according to ABC News America.

Rear Admiral Charles Williams, the commander of Task Force 70, offered his prayers for the sailor’s loss and thanked all those who participated in the search.

His name was being withheld pending notification of next of kin, the Navy said.

The search to locate the Sailor from #USSStethem reported missing in the South China Sea has been suspended. https://t.co/YH3aGqSsis

— 7th Fleet (@US7thFleet) August 5, 2017

China, which claims virtually all of the South China Sea, accused the US in July of trespassing in its waters when the USS Stethem sailed within 12 nautical miles of Triton Island in the Paracel islands, which are also claimed by Vietnam and Taiwan.

The operation was aimed at affirming the right to passage and challenging what the US considers China’s excessive territorial claims in the area.

China sent ships to intercept the destroyer.

China has strongly objected to repeated freedom of navigation missions by the US Navy in the South China Sea, where Beijing has rattled neighbours by constructing seven man-made islands in the disputed waters and fortifying them with radars and missiles.

—with AAP