Police have arrested a man in connection with alleged beatings that took place at the mosque in Keighley, West Yorkshire after secret footage shot for a Channel 4 "Dispatches" programme was posted on the internet.
The programme, "Lessons in Hate and Violence", which took two years to research and produce, was aired on national television on Monday night.
It also showed footage of xenophobic comments directed towards Hindus, Jews and Christians allegedly made by teachers at Darul Uloom Islamic High School in Birmingham.
Moderate Muslims came under attack there too.
"The person who's got less than a fistful of beard, then you should stay away from him the same way you should stay away from a serpent or a snake," a man described by the programme makers as a preacher is seen telling children.
The school is regularly inspected by the government and is required to teach tolerance and respect for other faiths.
Kicked and beaten
At the Keighley mosque, the Markazi Jamia Mosque, pupils as young as six and seven are seen on camera being kicked and beaten by teachers and teenage custodians during class. In one scene, a man with a long white beard raises his hand and slaps a young boy hard on the head.
Moments later he strikes another before kicking a third child. In just two days of filming last December, the camera recorded the teacher hitting children at least 10 times in fewer than three hours of lessons.
The programme alleges the beatings were common and that the two schools featured, out of more than 2,000 Islamic faith schools across the country, "taught intolerant and highly anti-social versions of Islam."
West Yorkshire Police said they were investigating and receiving co-operation from the Keighley Muslim Association.
In a statement, the Birmingham school said it had been unfairly targeted by the "surreptitious" recording and that the film had been selective in the material it had broadcast. It said students and teachers who were found to have contravened its high standards had already been expelled.
The Department of Education said it could not comment on individual cases but added: "any allegation of harsh physical punishment or the teaching of extremism in madrassas is very concerning."
A spokeswoman said the department was investigating the allegations and had taken legal advice over how to proceed.
The Muslim Council of Britain, an umbrella body representing 500 mosques and schools, said the documentary painted a "highly disturbing picture of Muslims experiencing intolerant teachings and violence in mosque schools."
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