There were five personnel on board the KC-130 and two on board the F/A-18 at the time of the incident, a Marine official told ABC News.
The Marine Corps tweeted that the incident occurred at about 02:00 on Thursday (17:00 GMT Wednesday). Search and rescue operations were underway at the scene. "The aviators retained their wings and will continue service to their country as valued members of 3rd Marine Aircraft Wing", he said.
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.
United States media also reported 5 crew on the C-130 and 2 on the F-18.
US military planes crash while refueling off Japan
"The circumstances of the mishap are now under investigation", the statement said.
"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 US military has about 50,000 troops stationed in Japan and accidents are not uncommon.
U.S. media say the two planes crashed during midair refuelling but this has not been officially confirmed.