The Defense Ministry said rescue workers are still searching for the jet and the five other crew members.
Only parts of equipment belonging to the jet and the airman, who was in a state of heart failure, were found in the mountains north of the Air Self-Defense Force's Kanoya base in southern Japan, according to the ministry. The location is believed to be near the area where the plane lost contact.
Ministry officials said the U-125 search-and-rescue jet disappeared from radar Wednesday while flying 10 kilometers (6 miles) north of the base.
World War II pilots took off on suicide missions from the base about 1,400 kilometers (870 miles) southwest of Tokyo.
Today, it is a key air base for reconnaissance activity for Japanese southern islands as China becomes more assertive in disputed waters.
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