An Air Self-Defense Force jet carrying six people disappeared from radar over Kagoshima Prefecture on Wednesday afternoon, the ASDF announced.
The U-125 disappeared from radar at around 2:35 p.m. while it was flying about 10 km north of the Maritime Self-Defense Force's Kanoya base in Kanoya, Kagoshima.
A Kanoya base official said the SDF was verifying a witness report of smoke rising near a mountain north of the base.
The SDF and local police terminated a helicopter search for the day at around 6:40 p.m., the police said.
Later on Wednesday, Defense Minister Gen Nakatani said the government will spare no effort to find the missing aircraft and rescue its crew members.
The jet was flying at an altitude of around 880 meters when it disappeared from radar, Nakatani said.
The U-125, a 15-meter-long twin-engine jet, is used by the ASDF to check on the condition of aircraft navigation facilities.
The missing aircraft, captained by a major in his 40s, belongs to the Flight Check Squadron at the ASDF's Iruma air base in Sayama, Saitama Prefecture. Other crew members included a second pilot, two onboard maintenance officials and two radio operations personnel.
It left the Kanoya base shortly after 1 p.m. and was scheduled to return at around 4 p.m.
There was thick cloud above the Kanoya base around 2 p.m., according to the Japan Meteorological Agency.
In February last year, an MSDF helicopter that left the Kanoya base crashed on a mountain in Ebino in neighboring Miyazaki Prefecture, killing three crew members.