He told MPs there were “genuine dangers” due to extremist influence in state schools - and revealed he had been working with Birmingham MP Khalid Mahmood (Lab Perry Barr) to counter the threat.
They have helped set up a series of workshops in inner-city Birmingham schools teaching students about Sufi music, which is inspired by poets who practiced Sufism, a mystical tradition within Islam.
Mr Mahmood said the aim was to teach young people about the true nature of Islam and counter the false impression they might get from extremists who deliberately target students.
The issue was raised in the House of Commons as MPs debated the Government’s policy of allowing parents and community groups to set up schools, known as free schools.
One Labour MP asked Mr Gove how he would prevent extremists setting up schools.
The Education Secretary said: “I have a consistent record of opposing Islamic extremism. One thing we have done is to set up a new due diligence unit within the department in order to ensure that the threat of extremism - not just from anyone who might wish to promote a free school, but from anyone who wishes to infiltrate our state school system - is dealt with.
“He will be aware that in both Surrey and Birmingham there were genuine dangers due extremist influence in state schools. I take the issue very seriously and I am delighted to work with others such as the member for Birmingham, Perry Barr in helping to counter it.”
Mr Gove added that it would be wrong to assume parents who wanted to set up free schools were extremists.
Mr Mahmood said: “I work with Michael Gove and have also spoken to Theresa May, the Home Secretary. It’s important that we work together across parties on issues like this.
“It’s not a response to a specific incident, more a general concern that young people are not being taught about Islam and this makes them vulnerable to extremists who pretend to teach them about their religion.”
Mr Mahmood said mosques tended to teach the Koran in Arabic which most young Muslims in Birmingham did not understand. This made it easier for extremist organisations to reach young people by talking to them in English.
The MP said he had been pushing for reforms to the way mosques operated, in particular by talking to young people in a language they understood.