The names of the girls, aged three and eight, have not been released. Their father was also in critical condition, along with a 12-year-old girl, police said.
Six people in all managed to escape the blaze, which was reported at about 4:40 a.m., said Quebec provincial police Sgt. Marc Tessier.
"For the other people involved, the man is in critical condition right now, plus we have another girl, age 12, she's also in critical condition," Tessier said.
"As for the mother, another six-year-old boy and a small baby, they are still at the hospital, but their lives are not in danger."
A visiting friend, a 12-year-old girl, also escaped the fire and was treated and released from hospital.
The two victims were found on the second floor.
The cause of the blaze has not yet been determined.
"It's too early," said Tessier, who noted the house was completely engulfed in flames by the time firefighters reached the scene.
"The six people that were inside, they all got out of the building by themselves. People tried to get back in the building to get the two persons who were left behind, but they weren't able to do it because of the intensity of the fire.''
Thurso is a community of about 2,500 people lying on the banks of the Ottawa River between Ottawa and Montreal. Its main claim to fame is that it's the birthplace of hockey star Guy Lafleur.