Posted on April 10, 2019
The pilot of the plane, however, is still missing, Japanese military officials said.
Parts of the plane have been recovered during search operations at sea.
It is not known why the plane, which is less than a year old, lost contact and crashed.
“We have collected parts from the jet fighter’s tail fin so we [believe] it crashed,” Defence Minister Takeshi Iwaya told reporters.
The fighter jet went missing at 19:27pm (10:27 GMT) on Tuesday as it was flying 135km (84 miles) east of Misawa, a city in north-eastern Japan.
It lost contact about 30 minutes after taking off from the Misawa Air Base.
According to Mr Iwaya, the missing pilot had sent a signal to abort the mission. All communication with him was lost shortly after.
Rescue teams are continuing their search for the male pilot who is in his 40s, according to news site Kyodo.
No problems with the aircraft had previously been reported, according to Japan’s public broadcaster NHK.
Japan has been deploying F-35s, which cost at least $90m (£68m), to replace its ageing F-4 fighter jet.