A Muslim leader in Oxford has accused the chief inspector of schools of "bullying" after he ordered Ofsted inspectors to mark down schools if the veil was acting as a barrier to learning.
Dr Hojjat Ramzy said the policy could lead to some Muslim students deciding to stay at home instead of attending class.
Sir Michael Wilshaw's warning that schools which allow pupils or teachers to wear the veil risk being failed by Ofsted came after Prime Minister David Cameron said last week that public organisations such as courts should be free to restrict the wearing of veils.
Dr Ramzy said Sir Michael's warning amounted to bullying.
The director of the Oxford Islamic Information Centre, and former chairman of the Education Committee of the Muslim Council of Britain, said: "As an Imam and educationalist, personally I do not encourage Muslim women to wear the face cover, however I do not discourage them either.
"It is a complete freedom of choice for women to dress as they please. In this country we enjoy the freedom to choose how we represent ourselves through our dress.
"As such, in the same breath, I condemn both those people who force women to wear the face cover, in places such as Afghanistan, and condemn Sir Michael Wilshaw who is forcing them to take it off.
"Students who are wearing the face cover are choosing to do so since they believe it is an important part of their practice.
"If they are forced to remove it, because their schools are threatened with being downgraded, they may choose to stay at home and not integrate to society, or may indeed be taken abroad where they will not receive the schooling they are entitled to as British citizens.
"Threatening schools with being degraded by Ofsted and blaming it on these innocent girls is an act of bullying.
"The wearing of the face cover should have no impact on teaching or learning, particularly since students’ eyes are uncovered so in no way is eye contact impaired.
"If there are instances where the wearing of the niqab may lead to issues of health and safety or impair the learning process, it should be left to the discretion of the headteachers, who are perfectly qualified to deal with such issues.
"Any decision to ask students to remove their face covers should come from the headteachers, not head of Ofsted."
Dr Ramzy added: "With these remarks, Sir Michael has caused even more tension and division between different faith groups in schools and in the wider community, at a time when we should be focusing on integration and understanding."
Stephen Evans, a spokesman for the National Secular Society, said the Government should set robust national guidelines.
He told The Times: "Full-face veils are obviously inappropriate in a classroom and inhibit communication between staff and pupils.
"There should be every expectation that pupils and staff can communicate and identify each other easily in schools.
"Such a prohibition in schools will also ensure that no young girls are compelled to wear the veil."
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