Muhammad Hussain, who was caught by the cleric while trying to run away, had been given corporal punishments in the past as well after he managed to flee the seminary in Bin Qasim Town, a senior police officer told PTI.
"His parents brought him back to the seminary and Qari Najmuddin took out his anger on the boy," the officer said.
"He was beaten with a blunt object and stick and there were visible marks of torture on his body," he said.
The parents have refused to allow a post-mortem examination of the child's body.
A case would be registered against the accused by the police.
Religious seminaries have mushroomed all over Pakistan and many parents who cannot afford to educate their children in schools, opt to send them to these seminaries.
In the recent past, some seminaries have been closed due to their suspected involvement in brainwashing young children and pushing them towards extremism and terrorism.
(With inputs from PTI)