Children who speak out in class against homosexuality could be viewed as potential extremists under Government guidelines intended to prevent Islamist terrorism, Nicky Morgan, the education secretary, has suggested.

Mrs Morgan said comments by children that they consider homosexuality to be “wrong” or “evil” could “trigger” concerns from teachers under guidance designed to help schools detect possible radicalisation.

Traditionalist Christians said Mrs Morgan’s remarks implied that anyone who raised their children in line with conservative religious teaching on sexuality would now be viewed with suspicion.

It follows moves to close two Christian schools after they were judged to have failed the Government’s new “British Values” tests introduced in the wake of the so-called “Trojan Horse” scandal in which hard-line Muslim groups attempted to infiltrate schools in Birmingham.

Ofsted inspectors have already been told to assess whether schools are promoting themes such as democracy, tolerance and the rule of law.

Writing in The Daily Telegraph this week, in the wake of the terrorist atrocity in Tunisia, David Cameron said Britain must be “intolerant of intolerance”.

The Department for Education has issued schools with new guidance to help identify pupils at risk of radicalisation.

Mrs Morgan said this would include “changes in behaviour” and “things that they say”.

Asked, during an interview on BBC Radio 4 if this meant that if a child questioned democracy a teacher would have to take action, she replied: “No, I think schools should be a safe space for young people to explore all sorts of ideas.

“But we have since last year been very clear that schools should also be teaching British values–those are the things that we all hold dear.”

She continued: “I think there are things like tolerance, and there are lines that young people or anyone else could tip over.”

Asked for an example, she said: “It could be for example, as we’ve seen, sadly Isil are extremely intolerant of homosexuality.”

Pressed on whether if a child said they believed homosexuality was “evil” or “wrong” that teachers might consider them a “danger”, she replied: “It could trigger a thought, it would depend very much on the context in which that was being discussed.

“But teachers would discuss it as they do already when they are concerned about children who are at risk of perhaps being drawn into a gang or being exploited or being neglected at home.

“This is a safeguarding issue.”

Andrea Williams, chief executive of the Christian Legal Centre, said: “Many families believe that marriage should only be between a man and a woman.

“Are these families now to be officially treated with suspicion and even linked with extremism?

“Are teachers going to be required to spy on them and even reported to the police?”

She added: “We are on the verge of a sinister new era of ‘thought-policing’ in our schools.”

Mrs Morgan, a practising Christian, voted against the legalisation of same-sex marriage but later said she had changed her mind.

A spokesman for the Department for Education said: “Teachers work with young people all the time and we trust them to recognise the difference between a young person expressing a personal belief of conscience and expressing intolerant, hateful or extremist views.

“This doesn’t and shouldn’t stop schools from discussing a wide range of issues, giving pupils a safe space to develop to explore a beliefs and ideologies and gain a proper preparation for life in modern Britain.”

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