Children freed by policemen after they raided a building in Daura, Nigeria - AP

Police have freed hundreds of manacled boys from a madrassa in northern Nigeria for the third time in a month, raising fears of systemic torture and sexual abuse in the region’s Islamic schools.

Officers leading a raid on the Mal Niga school in the city of Katsina late on Wednesday found more than 500 boys and young men, many of whom had been chained to walls, molested and beaten.

The discovery followed a pattern that has become grimly familiar in Nigeria’s mostly Muslim north. More than 1,200 males, some as young as five, have been freed in three police operations since late September.

In all three cases, many were found to have been beaten, starved, sexually abused and held in chains, sometimes for so long that they were unable to walk unaided after their rescue.

As in the previous two cases, Mal Niga separated its pupils. One building was well-kept and students living there were not regularly mistreated.

Fears have been raised of systemic torture and sexual abuse in the region’s Islamic schools Credit: Saddiq Mustapha/AP

But a second, filled with shackles, essentially functioned as a torture centre, a common feature at all three madrassas raided so far. Here inmates were held in chains and starved.

Newcomers and rebels were generally held in the second building, victims said, although students in the first were sometimes taken there to be beaten and molested.

The almost identical nature of the alleged abuse in the three madrassas, which are located across two separate states, has raised fears that the scale of the abuse could be much deeper than at first believed.

As many as 10m children are educated in privately owned madrassas across Nigeria, mostly in the north, according to Muslim Rights Concern, a local advocacy group.

Parents often send their children to private madrassas because they provide a better quality education than state schools — as well as providing more in-depth religious learning.

Adults also attend the schools, either to study the Koran or because they purport to offer university degrees.

Muhammadu Buhari, Nigeria’s president and a native of Katsina state, pledged to shut down madrassas in June before the abuses came to light. This week, he promised again to close those that treat students badly.

“The government cannot allow centres where people, male or female, are maltreated in the name of religion,” a spokesman for Mr Buhari said.

The owner and five members of staff at Mal Niga have been arrested, police said.