Both planes are usually based at a USA site in Iwakuni, west of Hiroshima, where numerous 50,000 American troops stationed in Japan also stay.
Both aircraft are reported to have crashed into the water. The search and rescue operations continue for the remaining six Marines.
A U.S. defense official told AFP there had been a crash after the plane took off from Marine Corps Air Station Iwakuni in southern Japan.
The Marine Corps suggested Japanese search and rescue aircraft had taken the lead on the rescue mission.
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A USA official, speaking on condition of anonymity, said it occurred during a refueling exercise.
The Marines refuel aircraft differently to the Air Force, said Carl Baker, executive director of the Pacific Forum think tank in Hawaii.
The circumstances of the mishap were under investigation and no other information was available, according to the statement.
The planes involved are a KC-130 and an F/A-18 based at Iwakuni near Hiroshima and were carrying seven personnel, Marines officials said.
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In November previous year, a C-2 cargo plane carrying 11 passengers and supplies from the base at Iwakuni to the aircraft carrier USS Ronald Reagan crashed during an annual bilateral maritime field-training exercise with the MSDF.
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.
The US military has about 50,000 troops stationed in Japan.
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