RCMP say it happened Saturday on the Norway House Cree Nation, more than 450 kilometres north of Winnipeg.
Investigators say the man responded to a knock on the door, and when he opened it he found an unknown male with his face covered.
The person at the door pulled out a firearm, and police say the resident shut the door.
Police say the suspect fired a number of shots through the closed door before fleeing.
The 23-year-old dad and his son were both struck in the lower body and have been transported to Winnipeg for treatment of non-life threatening injuries.
No arrests have been made.