The child vanished after leaving her home in the neighbourhood of Shahzad Town, in the capital Islamabad last week.
Her body was discovered in a nearby forest on Monday, five days after she disappeared.
The killing sparked huge protests in the city with many, including the girl's family, claiming the police did not act quickly enough.
Originally from the Pashtun minority Mohmand region bordering Afghanistan, her family refused to bury her body until a post-mortem examination was carried out, the Pakistan Today newspaper reported.
Officer Mohammad Imran said police chief Mohammad Abbas was suspended for failing to act promptly in the case and an investigation has been launched.
Two suspects have also been arrested in connection with the investigation into the girl's death.
Crimes against children are common in Pakistan and often go unpunished.
Associated Press contributed to this report