Sunday schools will be inspected by Ofsted "if there are concerns" with how they are run, the chief of the body has admitted.

Sir Michael Wilshaw, the Chief Inspector of Education, yesterday faced hostile questions on a radio phone-in over the government's proposals to allow Ofsted inspectors into out-of-school settings. The suggestion follows warnings that a small number of Muslim madrassas have been involved in radicalising young children.

However Wilshaw confirmed fears that Sunday schools could also face Ofsted inspections under the new regulations.

"If churches and religious groups want to run out of school classes then they need to register so the country and the Department of Education knows they are run properly," said Wilshaw in an interview with LBC radio yesterday.

"We won't be inspecting every one of them but we will know that they exist."

"If there are concerns and if whistle-blowers tell us there is an issue then we will go in and inspect," he said, marking a direct betrayal of the Conservative's manifesto promise to "reject any suggestions of sweeping, authoritarian measures that would threaten our hard-won freedoms."

Ofsted is not "the thought police," Wilshaw insisted, and said the "great majority of Sunday schools would not be affected".

"But", he told LBC's Nick Ferrari, "we need to know if a Sunday school is being run; is it registered and is it being run by people who have been put through proper safeguarding checks and if that is being done then we are happy.

"We will only go in when we feel there is a need to do so."

The comments come after a number of Conservative MPs said the regulations "could have a seriously detrimental effect on the freedom of religious organisations". In a letter to the Telegraph, they raised fears that Sunday schools and church youth groups could face sanctions from Ofsted if they taught that marriage was between a man and a woman.

"This would be an intolerable but very real possibility," the letter read, "given the clear desire of the Department for Education to investigate what it calls "prohibitive activities", such as "undesirable teaching... which undermines or is incompatible with fundamental British values".

"This could challenge established Christian teaching."

Wilshaw cited examples of certain "unregistered settings" Ofsted had seen where a "significant number" of young people were "being educated, living in appalling conditions in a filthy environment where there was homophobic literature, anti-semitic literature and misogynistic literature and where the staff have not been vetted".

"Children are at risk," he said.

When challenged that these were Muslim madrassas not Sunday schools, Wilshaw retorted, "we have to deal with this in an even handed way".

Wilshaw's comments could be seen as an embarrassment to the government as they directly contradict the assurances of an education minister who told peers in House of Lords yesterday: "we do not propose to regulate institutions such as Sunday schools and one-off residential settings which teach children for a short period every week."

A spokesperson for the Department of Education told Christian Today: "We recognise many out-of-school education settings do a great job in supporting children's education and our proposals are about making sure that in the small minority of cases where there are concerns raised by parents and others about issues of extremism, child cruelty or inappropriate teaching the government can take action to protect children.

"The Government is not proposing to regulate institutions teaching children for a short period every week, such as Sunday schools. We are looking specifically at places where children receive intensive education, to ensure that the children there are in a safe environment, which does not subject them to intolerant and hateful views." 

Dr David Landrum, director of advocacy at the Evangelical Alliance, said the proposals amounted to "the state regulation of private religion," however. Nola Leach, CEO of public policy charity CARE who have campaigned against the proposals, called Wilshaw's comments "staggering and revealing".

"This is a major breach of religious freedom and the alarming reality of an Ofsted inspector being sent into any Sunday School to question teachers and children is intrusive and wholly unnecessary," she told Christian Today.

"Ofsted does not assess the religious teaching of faith schools, so how extraordinary that it should consider assessing the religious teachings of churches in Sunday School," Leach added.

"Sunday Schools are places where children are being taught about the truths of the Bible, they are not training grounds for extremists."