The fighter jet went missing around 7:30 pm (1030 GMT) as it was flying some 135 kilometres (84 miles) east of Misawa, northeastern Japan, a ministry spokeswoman said.

The plane lost contact about 30 minutes after taking off from Misawa Air Base with three other aircraft.

It was not immediately clear if the aircraft had crashed, Defence Minister Takeshi Iwaya told reporters.

"First we are trying our best to carry out search and rescue operations," Iwaya said.

"And then we will do our best to probe the cause," he said, adding that Japan's 12 remaining F-35A fighters will be grounded for the time being.

The fate of the pilot was also unclear, a ministry spokesman said.

"A total of eight airplanes were sent to the area, but we have not received any information about the fighter," the spokesman said.

"We will continue our search and rescue operations all through the night."

The Self-Defence Forces and coastguard separately dispatched vessels to carry out rescue operations, he added.

Japan is deploying F-35As, each of which costs more than 10 billion yen ($90 million), to replace the ageing F-4 fighter jet.

An 80-member squadron of the stealth fighters was just formed last month at the base, according to Kyodo News.