Basti Kata, a resident of Mauza Ghunia in Rahim Yar Khan district, located 400 km from provincial capital Lahore, said his daughter went missing while playing outside his home on Thursday.
Kata informed police and registered a missing person's report. The girl's parents and other relatives made frantic efforts to find her but to no avail.
Yesterday, some of Kata's relatives found the girl's body in an open field. Police took the body to a state-run hospital in Khanpur, where the doctor on duty refused to perform an autopsy.
Hindus are the largest minority in Pakistan.
The aggrieved family staged a protest outside the hospital. Following the intervention of the local administration, the doctor conducted an autopsy that confirmed rape.
"It appears the girl died while being raped," the doctor said. Police have registered a case against unidentified persons. Hindus are the largest minority in Pakistan but make up only about two per cent of the population of 180 million.
Most Hindus live in southern Sindh province, where there have been several instances of alleged abduction and forced conversion of women from the minority community.
In Balochistan, which has a sizeable Hindu population, the community has been targeted by militants and criminal gangs in recent years.