Snap inspections of schools to see if they are teaching “British Values” have created an atmosphere of suspicion and mistrust, a Muslim leader has warned.

Dr Shuja Shafi, secretary general of the Muslim Council of Britain, told a London conference of head teachers that Muslims were happy to sign up to the teaching of values of fairness and tolerance saying that these were the “values of all of us” but said that the climate in which they had been published had led to many Muslims feeling their Britishness was under scrutiny.

Dr Shafi said: “This should not be a set of values achieved by some , the existing British population, which those who are not quite British enough must be civilised by.”

His comments came as Education Secretary Nicky Morgan said that tackling the threat of extremism in British schools was to be made a higher priority. In a statement to the House of Commons yesterday Ms Morgan said her department would extend the role of “counter extremism” in schools.

Education Secretary Nicky Morgan has said that tackling the threat of extremism in British schools is a high priority (Getty Images) (AFP/Getty)

Dr Shafi also defended the schools at the centre of the Trojan Horse scandal in Birmingham saying that they had been high-achieving before they were damaged by the allegations.

“Failures in governance and procedures do no equate to a caliphatic takeover. In getting to the bottom of the Trojan Horse allegations we missed an opportunity for community cohesion. Instead for too many Muslims it was another episode where Muslims are supposed to question where they belong when in fact they are as British as anyone else.

“Children in these schools were achieving highly and had promising futures. The so called Trojan Horse allegations undermined that and effectively destroyed their confidence.”

Dr Shafi was speaking at the 100 Group conference, a meeting of state and private school head teachers organised by the independent Brighton College and Kingsford Community School, a state comprehensive in east London.

Richard Cairns, head of Brighton College, told the conference about a state school where Muslim boys turned their backs on girls dancing in a school performance and insisted that they needed to leave their classrooms in the middle of lessons in order to pray at set times.

But Dr Shafi shocked heads when he said that was acceptable as long as the pupils did not show disrespect saying “they need to make their feelings known”, but after repeated questioning conceded that: “they should adopt the rules of the school”.

Joan Deslandes, head of Kingsford Community School, said schools experienced problems when trying to teach about statutory subjects such as gay rights because some parents would either keep their children at home on that day or lodge time-consuming complaints.