Marine Corps officials confirmed the incident but offered little information in a statement.
A spokesman for Japan's Self-Defense Forces said that one of the airmen had been rescued but the immediate fate of the remaining crew members was unclear.
A USA defense official told AFP there had been a crash after the plane took off from Marine Corps Air Station Iwakuni in southern Japan. Search and rescue operations were underway at the scene.
Japanese search-and-rescue aircraft immediately responded to the emergency, the statement added.
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The planes involved were an F-18 fighter and a C-130 tanker, the official said.
The Marine Corps said in a short statement that the incident occurred at 2 a.m. local time in Japan on Thursday (1700 GMT Wednesday).
The aircraft - a KC-130 and an F/A-18 Hornet - had launched from Marine Corps Air Station Iwakuni in southern Japan.
ABC News reported that a total of seven people were thought to be on the two aircraft. It was unclear if US military officials were also assisting with the search.
More than 50,000 USA troops are based in Japan under the bilateral security pact.