The boy, named Ryota, was rushed to hospital after the incident but died from blood loss, according to Nagoya local police.
A police spokesman declined to provide details of the motive, but explained: “The father stabbed his son in the chest with a kitchen knife.”
Kengo Satake, the child’s father, told police in Nagoya, capital of Japan’s Aichi Prefecture, he “argued with his son for not studying” for an entry test for a private junior high school.
He was arrested after local police received a phone call from hospital staff.
Mr Satake reportedly explained to police he stabbed his son “by mistake”, according to Japan Today.
The Satakes’ neighbours told police they used to occasionally see Ryota being locked out on the balcony as punishment for misbehaving.
The boy’s mother was at work when the incident took place, local media reported.
Competition for entry to the best schools in Japan is fierce. Admission to prestigious institutions is seen to have a direct correlation to a child’s future prospects.