There was no word yet on the fate of the one pilot on board the jet, Defence Minister Takeshi Iwaya said.

It was the first reported case of a crash by an F-35A, according to Japan's Air Self-Defence Force.

"We have collected part of its tail" in search operations at sea with planes and vessels, Iwaya told reporters.

"We believe it crashed," he added.

The fighter jet went missing around 7:30 pm (1030 GMT) Tuesday as it was flying some 135 kilometres (85 miles) east of Misawa, northeastern Japan, on a training mission.

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

"During the exercise, the aircraft... communicated that it was aborting the exercise, then communications from the plane stopped and its radar track disappeared," Iwaya said.

Japan's air force announced a commission late Tuesday to study the cause of the accident.

But it was still not clear exactly what happened to the plane by late Wednesday afternoon, a Japanese air force official told AFP.

US defence contractor Lockheed Martin touts the high-tech fighter as "virtually undetectable" and says it allows the US and its allies to dominate the skies with its "unmatched capability and unprecedented situational awareness."

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

The jet was one of 13 F-35As deployed at the base, according to the defence ministry.

The remaining 12 F-35A fighters have been grounded for the time being, the ministry said.

"Until we find out exactly what happened, it would be difficult for us to have those planes fly again," the air force official told AFP.

US military forces said they were helping the search-and-rescue effort.

"US Forces Japan will continue to work closely with the Japan Self Defence Forces and Ministry of Defence to assist with search and rescue efforts, as requested," US Forces Japan said in a statement.

The F35A jets are a key part of Prime Minister Shinzo Abe's efforts to upgrade the nation's military capacity to meet changing power dynamics in East Asia, with China rapidly modernising its military.

Over the next decade, Japan plans to purchase as many as 105 F-35As and 42 units of other high-capacity jets, most likely the F-35B variant.