The girl's post-mortem report concluded that she was first raped and then thrown off the roof of her house in Site Industrial Area of the city.
"Doctors have found evidence of sexual assault. She has sustained injuries on her head," said Seemi Jamali, the medico legal officer of Jinnah Hospital.
Jamali said the girl's body was sent for autopsy to the Civil Hospital due to absence of a female medico-legal officer at the Jinnah hospital.
Mubarak Pathan, a medico-legal officer at Civil Hospital, said the police were now investigating why the girl's family and relatives were reluctant for an autopsy.
"We are now investigating the matter," he said.
A researched report released by the Society for the Protection of the Rights of the Child stated earlier this year that 10 cases of child sexual abuse took place every day in Pakistan in 2015, bringing the total to 3,768 cases in 2015.