Yet parents of some of the boys have told The Daily Telegraph they knew what was going on in the madrassah cellars - and even approved of the brutal methods they believed were the only way to deal with teen delinquents.
One claimed to have aided the Madrassah Zakarya's approach. When Umar Khan took his two sons to the single-storey, whitewashed school, he brought with him two sets of chains and padlocks.
"They are young and so naughty. I was worried they would run away. This was to straighten them out for a month," he said.
The madrassah is now closed. Its head teacher is on the run and two members of the staff have been arrested. For now that means that Khan's two sons, Mohammed Haroon, 13, and Mohammed Shazwar, 10, have returned home.
"If they are naughty I'll send them to an even worse place where they are chained even tighter," he said, roaring with laughter.
Police arrived at the madrassah last Monday night alerted by a local television channel. As they prepared to raid the premises they could hear screams coming from beneath an open-air meeting room. They descended a stone staircase to find an underground warren of rooms - and unimaginable misery. They released more than 60 boys and young men living in squalor and chained to each other in threes.
Hooks sunk into the walls made the place resemble a "torture chamber" and 11 of the boys had been beaten "red and black", according to the police report.
Ehsan Marwat, who heads the local police station, said his officers were shocked at the welts and bruising they found.
"The police also use these methods but we have to face the courts and the media. These guys showed no mercy."
Mohammed Haroon said it was a relief to be going home. He had spent two weeks at the madrassah after being sent by his father for stealing a wheelbarrow from a neighbour.
"If we were being naughty then we would be beaten," he said, sitting on the steps in a dusty courtyard outside his former prison. "We knew that's how it worked."
The stairs to the dungeon have been sealed but that does not stop most of the madrassah's pupils congregating outside every day. Many have little choice if they want some form of education.
One of the youngest boys, Wali Mohammed, seven, had been asleep when the police arrived. The commotion sent him screaming from the scene - an image printed in newspapers around the world.
In a tiny voice he explained that he was never mistreated although he lived in fear of the noises he heard coming from underground.
"I never saw them and stayed away from the place because it sounded so bad," he said. "I knew they were down there because my brothers told me."
His father, Buaz Mohammed, admitted that he knew drug addicts were chained in the cellar but had no other option for his son's education.
"This was the only place I could send him because they don't ask for any money."
The mosque stands in Sohrab Goth, a desperately poor corner of Karachi, Pakistan's economic capital. Thousands of people have arrived from Afghanistan, the border areas and the province of Balochistan looking for work and living in little more than a shanty town.
