"US Navy and Japan Maritime Self-Defense-Force ships and aircraft are searching for a sailor from USS Stethem reported missing while the ship was conducting routine operations in the South China Sea" early Tuesday, the US 7th Fleet said in a statement.
"Multiple searches were conducted inside the ship but were unable to locate the sailor," it said.
Japan's Maritime Self-Defense Force, the country's navy, confirmed two of its vessels as well as helicopters have been taking part in the search.
The two nations have called off their routine joint operation to focus on the search, a Japanese navy spokesman told AFP.
The sailor's name is being withheld while the search is ongoing and the exact location of the search was not disclosed.
The incident comes weeks after seven American sailors were killed when their Navy destroyer collided with a Philippine-flagged cargo ship in a busy shipping channel off Japan's coast.
Aged 19 to 37, the seamen were found by divers in flooded sleeping berths a day after the collision tore a huge gash in the side of the USS Fitzgerald.
Japanese and US naval forces have been holding drills in the contested South China Sea in the face of Beijing's increasing assertiveness over its maritime claims in the region.
China is also involved in a simmering territorial row with Tokyo over disputed islands in the East China Sea.
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