The fighter jet went missing at around 7:30 pm (1030 GMT) as it was flying some 135 kilometres (84 miles) east of Misawa, northeastern Japan, a ministry spokesperson said.
It was not immediately clear if it had it crashed, the spokeswoman said, adding: "We are still trying to search for the aircraft."
The fate of the pilot was not immediately clear.
The plane lost contact about 30 minutes after taking off from Misawa Air Base, public broadcaster NHK said.
今夜、青森県三沢市沖の太平洋上で航空自衛隊の最新鋭の戦闘機、F35Aの機影がレーダーから消え、航空自衛隊が詳しい状況の確認を急いでいます。
— NHKニュース (@nhk_news) April 9, 2019
(映像はF35Aの資料映像 三沢基地 去年1月撮影)https://t.co/79oe5QhKws pic.twitter.com/8fS4VfOWxh
The Self-Defence Forces and coastguard dispatched vessels to carry out rescue operations, NHK added.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ