Defence Minister Takeshi Iwaya told reporters the search had been halted but that his teams were still investigating the cause of the crash, adding that F-35A operations in northern Japan had not yet resumed.

The ministry would also keep monitoring a wider area with underwater cameras "for the purpose of protecting classified military information," Iwaya said.

Experts say Japan and the US are keen to prevent sensitive debris from the plane being recovered by Russia or China, and Iwaya himself has admitted there were "a significant amount of secrets that need to be protected" on the jet.

Some debris have been recovered, including the jet's tail, but neither the pilot's body nor the flight data recorder have been found.

The state-of-the-art fighter jet went missing on April 9 while flying 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.

It was the first reported crash by an F35-A, according to Japan's Air Self-Defence Force.

Japan is deploying F35-As, each of which costs more than 10 billion yen ($90 million), to replace its ageing F-4 fighters.

They 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.