The U.S. Marine Corps said that the 2 a.m. crash involved an F/A-18 fighter jet and a KC-130 refueling aircraft during regular training after the planes took off from their base in Iwakuni, near Hiroshima in western Japan.
The crash took place 320 kilometers (200 miles) off the coast.
Japan's Defense Ministry said the aircraft carrying seven crew members in total collided and crashed into the sea south of the Muroto Cape on Shikoku island in southwestern Japan.
The Maritime Self-Defense Force, which dispatched aircraft and vessels to join in the search operation, said Japanese rescuers found one of the crew members in stable condition. The Marine Corps said the rescued crew was taken to a hospital at its base in Iwakuni and was being treated, but did not provide any other details.
Japanese officials said two crew members were in the F/A-18, and five others in the KC-130.
The crash is the latest in recent series of accidents involving the U.S. military deployed to and near Japan.
Last month, a U.S. Navy F/A-18 Hornet from the aircraft carrier USS Ronald Reagan crashed into the sea southwest of Japan's southern island of Okinawa, though its two pilots were rescued safely. In mid-October, a MH-60 Seahawk also belonging to the Ronald Reagan crashed off the Philippine Sea shortly after takeoff, causing non-fatal injuries to a dozen sailors.
More than 50,000 U.S. troops are based in Japan under the bilateral security pact.