A well-known doctor, Junichi Suzuki, 44, was shot and held hostage, police said. He later died in hospital.
Crimes committed with a firearm of this severity are rare in Japan where firearms are heavily regulated.
It is unclear what led to the violence or how the suspect had a firearm, reported as a hunting weapon by some media outlets. The police have launched an investigation.
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Japanese media reported that the medical team attended to the suspect’s mother, who died recently.
The group had paid a compassionate visit to the man’s home on Thursday evening at his request, the Japan Times reported.
Police were first alerted around 9:00 p.m. local time (1200 GMT) after neighbors reported gunshots and found a man bleeding from chest and stomach wounds outside the house.
The 41-year-old male nurse was taken to hospital where he remains in critical condition, police said.
Another man, 32, had managed to flee the house to a police station, media reported.
Police advanced on the house that night, according to reports.
Police in riot protection rushed to cover the house during the hostage crisis.
The 11 a.m. siege took place in a town just north of Tokyo.
Officers spoke with the shooter throughout the night by phone, but he made no inquiries or requests, local media reported.
On Friday morning, while the siege was still ongoing, authorities evacuated about 110 residents from the neighborhood and closed nearby schools.
Police stormed the house soon after, where they found Mr. Suzuki and arrested the suspect.