The incident occurred Sunday at Bholakheda here. Kamal Kishore Tiwari, 27, a priest, went to the grocery shop owned by the boy's father to buy milk.
The boy's mother said there was no milk. But the priest would not take no for an answer. When the woman refused to give him milk, he caught hold of her in anger.
Seeing the commotion, the 12-year-old rushed into the house and returned with a single barrel gun to which his father held the licence. Tiwari was shot in the stomach.
Neighbours rushed a profusely bleeding Tiwari to hospital, where he succumbed to the injury.
The boy has been arrested. Since he is a minor, police said he would be sent to a juvenile home.