The governors of a dysfunctional Muslim free school got things "very badly wrong" Michael Gove has said.
The Education Secretary said the Government had taken swift action to step in after whistle-blowers raised concerns earlier this year about the running of the Al-Madinah School in Derby, including claims girls were made to sit at the back classrooms during lessons.
Last month the school was condemned by Ofsted inspectors, who said its governing body was ineffective and had failed to appreciate how poor pupils' experiences are.
On Friday, the school's trustees agreed to resign and a new headteacher and trust board have now been brought in to turn the school around.
Mr Gove said Al-Madinah School was the exception rather than the rule and that free schools and the wider reforms he introduced were moving the education system in the right direction.
He also suggested there would be greater scrutiny of faith-based free schools in future saying: "We do need to police carefully, schools which do have a faith ethos and I'll be saying more about that in due course,"
He added there were "outstanding" faith-based free school across the country.
Mr Gove said in the case of the Al-Madinah School it had been important to show the Government could react "quickly" once problems had come to light.
Speaking on BBC's The Andrew Marr Show, he said: "For me the test is how quickly do you deal with with failure and we recognised very quickly after a whistle-blower brought to our attention some real concerns with this school that we needed to take action.
"Just last week we were able to say the current group of governors - idealistic people, but people who got it badly wrong - are now standing down and there's a great new headteacher who's taking over.
"So that's the first test I set myself - the speed with which you deal with failure.
"But the second test is: have free schools and have our reforms started to move the education system in the right direction, and I think overall they have."
Asked about concerns over the numbers of unqualified teachers in free schools, Mr Gove said there were now fewer unqualified teachers in state schools than there were under the previous Government.
He added: "There are some teachers in free schools who do not have what's called the 'Qualified teacher status' which is a particular type of teaching qualification but the same thing is true in independent schools, fee-paying schools and the fact is that some of the free schools are independent schools that have come into the state system."
Mr Gove said the education reforms were about creating a more equal society where all pupils were given the same opportunities, whatever their background.
"We've got a big problem in this country, in that England has for generations now has been stratified and segregated because of an unequal education system," he said.
"Free schools are a part of changing that.
"They are bringing good schools to areas where there has been under-performance in the past but we're making other changes as well, with our Liberal Democrat colleagues.
"We're spending more money on the education of the very poorest children and we're also changing the curriculum so it embeds a higher level of ambition."
On the wider subject of faith-based free schools, he said: "We do need to police carefully schools which do have a faith ethos and I'll be saying more about that in due course.
"But let's not forget the fact there are outstanding schools which have a faith ethos in different parts of the country."
He added: "The whole point about state faith schools is that they strike the right balance between respect for the many great faiths that make modern, multi-cultural Britain but at the same time, through proper inspection and adherence to a broad and balanced curriculum, we make sure the children can respect their heritage and then be fully integrated into modern Britain."
Earlier this year, whistle-blowers at Al-Madinah School claimed non-Muslim female staff were being pressured to wear head scarves, while girls were made to sit at the back of classrooms during lessons.
Last month, Ofsted inspectors branded the school "dysfunctional" and order it placed in special measures, while a separate audit found poor financial governance in place.