Rescuers have recovered two of the seven crew members involved in the crash, which occurred during routine refueling training around 2:00 a.m. local time.
While one of the Marines is in fair condition, "the other has been declared deceased by competent medical personnel," officials said.
"The search-and-rescue operations continue for the remaining five U.S. Marines who were aboard the KC-130 Hercules and F/A-18 Hornet," III Marine Expeditionary Force said in a statement Thursday. "As to what was taking place when the mishap occurred, that is under investigation."
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The aircraft launched from Marine Corps Air Station Iwakuni early Thursday morning. The accident occurred about 200 miles off the coast of Japan, officials said.
The Marine in stable condition is reportedly one of the F/A-18 pilots, according to Military Times.
The pilot was rescued by an SH-60 Sea Hawk crew assisting in the recovery, the paper said, adding that debris has been found.
The Japan Maritime Self-Defense Force and the Japanese Coast Guard are also providing assistance, III MEF said. That includes Japanese ships, a submarine and helicopters, according to Military Times.
C-130 Hercules crews from Yokota Air Base are on alert, awaiting orders to circle above the crash site and search for survivors, officials told Military Times.