The deceased were men aged 18 and 36, Edwards said. He did not confirm a WWBT television news report that the victims were father and son.
The suspect is the son of the head of the Nakano city council, public broadcaster NHK reported.
The individuals involved were brought before the commander of Sayeret Nahal, Col. Oren Simcha, on Sunday to receive final judgment.
Two officers were wounded in an exchange of gunfire with the suspect, who was killed at the scene, and there were multiple civilian victims, at least three of whom died.
Two officers from a five-member team shot the assailant in a lobby area, and the suspect was pronounced dead by 10:27 a.m.
One attacker was killed on the scene while searches are ongoing for another possible attacker, who may have fled.
The officer's father and brother were also arrested.
A 17-year-old mother, her baby, and 5 other members of the family have died from the shooting
School officials searched the child's backpack the day he shot his teacher, but did not find the gun.
The injury to the teacher was considered life-threatening, though she had shown some improvement in the hospital.
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