Schools are refusing to take part in a Government counter-terrorism strategy which asks them to identify Muslim pupils at risk of being radicalised, The TES has learnt.
The pound;12.5 million "Channel" project was set up to prevent young people being recruited by violent extremists. As part of the initiative, teachers have been asked to report vulnerable pupils to panels established by counter-terrorism police.
But there is widespread feeling among teachers that taking part in the scheme, which includes around 7,500 schools, risks damaging relationships in the classroom and community.
Ted Cantle, executive chair of the Institute of Community Cohesion, said that most teachers do not want to be involved.
"Schools have refused to take part in Channel, only very few schools have done so," said Professor Cantle, who was appointed by the Home Office to chair its community cohesion review team.
"Most teachers are very reluctant to get involved with preventing violent extremism in that level of detail. They feel they don't have the skills to identify those at risk accurately, and they feel it would destroy the trust they develop with pupils."
A recent Commons select committee report found that wider preventative strategies were alienating Muslim communities because they were perceived as "spying".
Mick Brookes, general secretary of the National Association of Headteachers, said he would advise his members to be "extremely cautious" about becoming involved in counter terrorism work.
"You have to be careful it doesn't create an anti-Islamic ethos and is perceived as an anti-Muslim activity," he said. "I understand the need to be alert, but I find it difficult to see how this work can work in schools without it being damaging and making people feel they are under suspicion."
Chris Keates, general secretary of the NASUWT, said: "Teachers are not guardians of national security. Their job is to create a safe environment and ensure children's wellbeing.
"Some of our members are uncomfortable with what they see as an over- emphasis on the Islamic community and are concerned at the effects of this."
So far 228 children have been identified as needing "mentorship or challenge" since Channel began in autumn 2007. None has been charged with any offences by the police.
The project was originally piloted in Lancashire and the London borough of Lambeth in 2007, but was extended to West Yorkshire, the Midlands, Bedfordshire and South Wales two years ago.
Despite the concerns, John Dunford, general secretary of the Association of Schools and College Leaders, said schools have a "moral duty" to help the police.
Ian Fenn, head of Burnage Media and Arts College in Manchester and the city's lead headteacher on preventing violent extremism, said: "I can understand why teachers are wary and shying away if they don't feel they have the expertise," he said. "But we look at this work as the same as safeguarding, something all schools are now very skilled at.
"We have a close relationship with police, we trust them and we always ask why when they make a request of us."