ABC News reported that a total of seven people were thought to be on the two aircraft.
The recovered crewmember was being evaluated by medical authorities at Marine Corps Air Station Iwakuni, according to a III Marine Expeditionary Force statement issued just before 9 a.m. local time.
But officials said the two pilots, whose names were not released, will be allowed to keep their wings, according to the Marine Corps Times.
It was unclear if USA military officials were also assisting with the search.
The incident is under investigation, the Marine Corps said. The search and rescue operations continue for the remaining six Marines.
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A Marine Fighter Attack Squadron 224 F/A-18 Hornet conducts an aerial refuel utilizing a KC-130J in coorlation with Weapons and Tactics Instructor Course in Yuma, Ariz., April 10.
A crash may have occurred mid-air during the refuelling but this is unconfirmed.
"The circumstances of the mishap are now under investigation".
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.
However, refueling is a unsafe operation, Baker said.
The US has more than 50,000 troops stationed in Japan, more than 18,000 of them in the US Marine Corps.