The pilot of the aircraft is still missing, said the Air Self Defence Force (ASDF) spokesman.

A Japan's Self-Defence Forces F-35A stealth fighter jet at Misawa airport in Aomori prefecture, on Jan 26, 2018. (Photo: AFP/Jiji Press)

"We recovered the wreckage and determined it was from the F-35," the spokesman told Reuters.

The F-35 was less than a year old and was delivered to the ASDF in May last year, he added.

Japan's first squadron of F-35s has just become operational at the Misawa air base and the government plans to buy 87 of the stealth fighters to modernise its air defences as China's military power grows.

The advanced single-seat jet was flying about 135 km east of the air base in Aomori Prefecture at about 7.27pm (5.27pm, Hanoi time) on Tuesday, when it disappeared from radar, the Air Self Defence Force said.

Lockheed Martin said in a statement that it was standing by to support the Japanese Air Self Defence Force as needed.

The Pentagon said it was monitoring the situation.

The crash was only the second time an F-35 has gone down since the plane began flying almost two decades ago. It was also the first crash of an A version of the fifth-generation fighter designed to penetrate enemy defences by evading radar detection.

A US military short take off and landing (STOVL) F-35B crashed near the Marine Corps Air Station Beaufort in South Carolina in September prompting a temporary grounding of the aircraft. Lockheed Martin also makes a C version of the fighter designed to operate off carriers.

Japan's new F-35s will include 18 short take off and vertical landing (STOVL) B variants that planners want to deploy on its islands along the edge of the East China Sea.

The F-35s are shipped to Japan by Lockheed Martin and assembled by Mitsubishi Heavy Industries Ltd at a plant near Nagoya in central Japan. Each costs around US$100 million, slightly more than the cost of buying a fully assembled plane./.

VNF/AFP