The independent Darul Uloom School in Birmingham is featured in a Channel 4 Dispatches investigation called Lessons in Hatred and Violence.
According to Channel 4, the programme shows secret footage of adults at the school teaching pupils as young as 11 contempt for other religions and wider society.
A spokesman for the school has fiercely denied the claims, but confirmed that the school would close for two weeks from the 15 February, to protect pupils in the aftermath of the programme.
A statement from the school said Channel 4 had targeted them unfairly by "surreptitiously recording" inside the school for longer than six months.
"Over that period of time they have selectively gathered a handful of quotes and comments allegedly from some teachers, which they are using to attempt to portray our school in a light completely contrary to its ethos," the statement explained.
"No school can claim to be immune from incidents that require remedial action. What we have demonstrated repeatedly is that our procedures have dealt with contraventions in the past, and will continue to do so. These actions have included expulsions of students, and dismissals of teachers, as long as six months prior to us having knowledge of the surreptitious recording."
But Channel 4 defended its investigation, as being "clearly in the public interest". Its spokesman said: "We stand by our investigation and think the programme speaks for itself."
A joint statement from Birmingham City Council and the West Midlands Police pledged to tackle any safeguarding issues raised as a result of the programme.
In 2009, the Bridge Schools Inspectorate rated Darul Uloom as an improving school with a number of positive features.
"Pupils learn about the beliefs and practices of other faiths and are taught to show respect to other world religions," the report said.
The Department for Education insisted that inspections of independent faith schools are rigorous.
"All school inspections are carried out by appropriately trained and qualified inspectors," a spokeswoman said.
"In the case of faith schools, inspectors have the experience, knowledge of the faith curriculum and the language skills needed to inspect independent faith schools with the rigour and objectivity required."
