The chief inspector of schools Sir Michael Wilshaw has defended himself against accusations that he is presiding over a state-sponsored anti-faith school "witch hunt".

Sir Michael, a former headteacher of a Catholic secondary school, said the allegation would be "laughable" were it not so serious.

Writing in the Independent, he said: "I have long been a staunch supporter and proponent of faith schools in this country, believing that they are a valuable and enduring feature of our education landscape."

He agreed that Ofsted is not perfect and should not be above criticism. "But I can't help feeling that some of the criticism is being used as a smokescreen for the palpable weaknesses of leadership and management that inspectors sometimes observe."

His comments came after a row that follows decisions by inspectors to fail two Christian schools, Durham Free School and Grindon Hall in Sunderland, for failing to show respect to people of other faiths and for instances of homophobic bullying. The two schools were also criticised for their standards of teacher.

Durham Free School, which is still receiving applications from parents who wish their children to attend, has had its funding withdrawn and faces closure at Easter.

The school said this week it had made formal representations to education secretary Nicky Morgan. The school is seeking a judicial review of the closure decision and has also made a formal complaint about the conduct of the Ofsted inspection in November.

Following the so-called Trojan Horse affair, when allegations were made about a supposed plot by extremists to take over a non-faith state school in Birmingham, the Government told Ofsted that all schools must teach "British values" to prepare pupils for life in modern Britain.

Muslim schools have also been criticised. Five private schools in Tower Hamlets, east London, were recently declared "failing".

Sir Michael wrote: "Let me offer this unequivocal reassurance – the vast majority of faith schools have nothing to fear either from Ofsted or from the recent guidance issued by the Department for Education on promoting British values as part of the curriculum.

"But don't just take my word for it. Since the start of this academic year alone, Ofsted has inspected approximately 600 schools with a religious designation or character. Many of these schools have drawn praise from inspectors for quietly getting on with the task of ensuring all their children are being prepared for life in the complex, diverse society in which we now live."

He praised schools such as Sinai Jewish Primary School in Brent, where inspectors found that pupils are "proud to be Jewish" but also "enjoy working with pupils from different ethnic and religious backgrounds."

He also praised St Ethelbert's Catholic Primary in Slough, where last month inspectors praised a curriculum that "encourages pupils to see the world from different perspectives and has the notion of tolerance and mutual respect running through its core."

Sir Michael continued: "There seems to be a tendency on the part of an unrepresentative handful of schools – and their defenders – to presume that they are speaking up for many others by accusing Ofsted of all manner of inappropriate conduct and dubious motives."