The family's mother and their three-year-old girl were also taken to hospital with serious injuries.
Police said the family of five was found unconscious at the site of the fire _ an apartment in a four-unit building in Ste-Therese, a suburb northwest of Montreal.
Fire crews and police arrived at the scene at 7:20 a.m.
Sgt. Martin Charron, a spokesman for the local force, said they received a call reporting that thick white smoke was seeping out of the building.
"When police entered into one of the units they found five people unconscious on the floor," Charron said.
"We're talking about two adults and three young children."
The family was quickly rushed to a nearby hospital, and later transferred to hospitals in Montreal to be treated by specialists. Charron said the father and the two boys remained in critical condition Saturday afternoon.
Three police officers were also hospitalized with smoke inhalation.
It took about an hour for firefighters to put out the flames, Charron said.
By midday, the residential street was quiet and the front of the building showed little damage.
Investigators were still trying to determine the cause of the fire.