The planes involved are a KC-130 and an F/A 18, carrying a total of seven personnel, USA media quoted officials as saying.
The incident occurred about 200 miles off the coast of Iwakuni at 2 a.m. on Thursday, or about noon Wednesday, Eastern Standard Time.
The C-130 was thought to be carrying 5 servicemen and the F-18 two, said the Japanese official, who added that Japan had scrambled 4 aircraft and 3 ships in the search. It was unclear if US military officials were also assisting with the search.
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"We are thankful for the Japan Maritime Self-Defense Force's efforts as they immediately responded in the search and rescue operation", the Marines said.
The survivor is being assessed by doctors at MCAS Iwakuni.
He says it is not clear what the weather conditions were like but overnight there was widespread cloud and rain across the Japanese archipelago. Two aviators were on the F/A-18 Hornet, while five Marines were on the KC-130.
The Marine Corps offered little information in a statement about the incident.