Officers with Surêté du Québec were called to a residence in Thurso on Wednesday, where they found a newborn with symptoms of shaken baby syndrome.
The baby was taken to a hospital in nearby Buckingham, Que., then transferred to Ottawa, where she died Friday night.
The father appeared in court in Gatineau, Que., on Thursday on one charge of aggravated assault.
Sgt. Christine Coulombe said the man could face further accusations, pending the result of an autopsy.
Marc-André Cayen, the lawyer representing the baby's father, said he doesn't have a criminal record and had never been arrested before this week.
"It's a situation that's difficult for everyone," Cayen said.