A 15-year-old girl died early Tuesday after hanging herself in a bathroom at her high school Sunday afternoon, police said.
The girl had been taken to a hospital where she remained in a coma.
The school, which is run by Nagasaki Prefecture, is investigating the incident.
The girl had been quarreling with friends in her brass band club, but the school's principal said that it was unlikely bullying was a factor in her death.
The school held a student assembly Tuesday morning and offered a silent prayer for the girl.