Muhammad Hussain, who was caught by the cleric while trying to run away, had been given corporal punishment in the past as well after he managed to flee the seminary in Bin Qasim Town, a senior police officer said yesterday.
"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 police said that they would register a case against Najmuddin.
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Religious seminaries have mushroomed all over Pakistan and many parents, who are poor and can't afford to educate their children in schools, opt to send them to these seminaries run by Islamic groups.
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.
Earlier, a TV channel had showed students being chained in a room of a seminary in Sohrab Goth.