Authorities were called early Saturday by someone close to the pair who hadn’t been able to reach the women for several days.
The sisters have been identified as Louise and Solange Paquet, aged 68 and 72.
SQ spokesman Daniel Thibaudeau said police found the body of one of the women as soon as they entered the house Saturday morning. The second body was found later in the afternoon.
Investigators spent all day Saturday at the scene, trying to determine the course of events.
Neighbours described the women as being somewhat reclusive.
"They're women that you didn't see at church or at the caisse populaire or at the store," said Michel Chartrand. "They never had visitors, there were never any cars about. I think they were very fearful."
"They were very reserved women," said another neighbour, Nathalie Lemelin. "You might see them in their yard, but they weren't very neighbourly. They were very discreet."
Police say they are considering several possible hypotheses while they wait for the autopsy results to determine the cause of the deaths, which they are considering suspicious.
Thibaudeau said investigators are not looking for any witnesses.