Two soldiers were killed and a third wounded when a fellow recruit opened fire at a training range in central Japan on Wednesday, the military said.
"During a live-bullet exercise as part of new personnel training, one Self-Defense Forces candidate fired at three personnel," the Ground Self-Defense Force (GSDF) said in a statement.
"The death of another person has been confirmed of the three who were shot at," the GSDF added later, after earlier announcing a first death and two injuries.
Earlier, government spokesman Hirokazu Matsuno said a suspect had been detained, but gave no further details.
Local police told AFP the shooter was an 18-year-old SDF candidate who was detained on the spot by other soldiers.
He has been charged with the attempted murder of a 25-year-old soldier, a local police spokesman said, declining to be identified.
The suspect "fired a rifle at the victim with the intent to kill", the spokesman told AFP.
National broadcaster NHK reported the wounded were a man in his fifties and two other men in their twenties.
Aerial footage broadcast by the station showed military and civilians gathered around an emergency vehicle and police blocking nearby roads.
Some appeared to be investigators, wearing covers over their shoes and hair.
A local resident told NHK he saw several emergency vehicles rushing to the area at around 9.30am local time (0030 GMT) but had not heard anything before that.
The training range is administered by the region's Camp Moriyama and is a covered facility of more than 65,000 square metres.
Violent crime in Japan is extremely rare and gun possession tightly controlled.
But several high-profile incidents have rattled the country over the last year.
In July 2022, former prime minister Shinzo Abe was shot dead on the campaign trail by a man who allegedly targeted him over his links to the Unification Church.
The accused assassin, Tetsuya Yamagami, was due to make his first appearance in court this week, but the session was cancelled after a package sent to the facility set off a metal detector.
It was later found to contain no explosives, but rather a petition signed by thousands calling for a lenient sentence for Yamagami.
He has garnered surprising sympathy from some quarters over the effect his mother's devotion to the Unification Church had on his family and childhood.
In April, Prime Minister Fumio Kishida escaped unharmed after a man threw an explosive device towards him at a campaign event.
That incident came shortly before Japan hosted the Group of Seven leaders' summit in Hiroshima and prompted renewed calls for stepped-up security.
Thousands of police were deployed to secure the gathering, which passed without a security incident.
Last month, police in the Nagano region west of Tokyo detained a man after an hours-long knife and shooting rampage, followed by an extended stand-off.
The man killed four people, including two police officers, before he was detained. He is reportedly the son of the speaker of the local city assembly.