The KC-130 also can be used to transport ground troops.
Japanese search and rescue aircraft "immediately responded to aid in recovery", it said, adding that circumstances of the incident were now under investigation.
The aircraft - a KC-130 and an F/A-18 Hornet - had launched from Marine Corps Air Station Iwakuni in southern Japan.
The Marine Corps tweeted that the incident occurred at about 02:00 on Thursday (17:00 GMT Wednesday).
A United States official, speaking on condition of anonymity, said it occurred during a refueling exercise. It is not known at this time if the aircraft was refueling at the time of the crash. The search and rescue operations continue for the remaining six Marines.
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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 rescued crew member was taken to the Marine Corps Air Station Iwakuni in western Japan, the Marines said.
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It said in a statement that the accident is under investigation and gave no further details.
In July 2017, a KC-130T crashed in MS while flying from Stewart Air National Guard Base in NY to Naval Air Facility El Centro in California, killing all 16 Marines and prompting the military to ground many other C-130s afterward.