The pilot is still missing. The F-35A stealth jet disappeared from radar while flying off the eastern coast of Aomori. Parts of the jet were found late Tuesday, the Air Self-Defense Force said.
It went missing about half an hour after taking off from the Misawa air base with three other F-35As.
Defense Minister Takeshi Iwaya told reporters the cause of the crash was not immediately known. He said 12 other F-35s at the Misawa base would be grounded.
The pilot is a man in his 40s, Iwaya said.
Under guidelines approved in December, Prime Minister Shinzo Abe's government plans to buy 147 F-35s, including 105 F-35As, costing about 10 billion yen ($90 million) each.