The Lockheed Martin F-35A stealth jet had been flying just off the eastern coast of Aomori, northern Japan. Since it emerged that the jet had disappeared crews had found wreckage in water near to the water the jet had been close to. The Air Self Defense Force (ASDF) confirmed the wreckage was that of the missing jet.
However, its spokesman said the pilot remained missing.
Lockheed Martin, the manufacturer, added that it was standing by to support the Japanese ASDF.
According to News.com.au, Japanese defence minister Takeshi Iwaya told reports the rescue operation was underway but the cause remained unclear.
The pilot is reported to be a man in his 40s who went down with the plane.
Mr Iwaya added: “First we are trying our best to carry out search and rescue operations.
“And then we will do our best to probe the cause.
“A total of eight aeroplanes were sent to the area, but we have not received any information about the fighter.”
The jet had been flying around 84 miles east of the airbase in Aomori Prefecture at approximately 7.30pm local time (10.30pm GMT).
The flight then disappeared from radar.
If the flight had crashed it would become only the second time an F-35 has gone down since it becoming operational 20 years ago.
The last time this happened the plane crashed near the Marine Corps Air Station Beaufort, South Carolina.
That incident took place in September and prompted a temporary grounding of the aircraft.
Reports suggest that the plane lost contact about 30 minutes after taking off from the airbase along with three other aircraft.