Education hit squads are being sent into schools to root out conservative Islamic practices, according to reports.
Michael Gove wants inspectors to fail schools where religion is "getting in the way of learning and a balanced curriculum", The Sunday Times said.
Under the plans headteachers and governing bodies could be replaced by teams chosen by Whitehall officials.
"Extreme religious conservatism often acts as an entry to later problems," a Department for Education source told The Sunday Times.
"A child who is brought up, age eight, nine, 10, believing that you should segregate the sexes and hand out Islamic textbooks is more likely to be radicalised in later life.
"In our view female staff being bullied in schools and segregated assemblies are very serious matters."
It follows a pledge by Prime Minister David Cameron earlier this month that sw ift action would be taken against any school found to be ''run by extremists'' as investigations began into an alleged ''Trojan Horse'' plot by Muslim hardliners to seize control of schools in Birmingham.
Park View Academy - one of several schools at the centre of the claims - has dismissed allegations of forced segregation and promotion of al Qaida as an anti-Islam ''witch hunt'' and insisted there was ''no evidence for any of these things whatsoever''.
Birmingham City Council, the Department for Education and Ofsted have been to a number of schools in the city as part of the probe, initially prompted by a letter claiming responsibility for ''disrupting'' the leadership of several institutions.
If enough of them are judged to be "inadequate" the Education Secretary wants a wave of new investigations to be launched across state and private schools, according to the newspaper.
"The investigations will be done over several phases over the next few months and will help narrow down the schools that require further investigation by the DfE and those that are deemed OK and not connected to the Islamicisation," a Whitehall source told the newspaper.
A DfE spokesman said: " The allegations made in relation to some schools in Birmingham are very serious and we are investigating all evidence put to us in conjunction with Ofsted, Birmingham City Council and the police. It is absolutely vital these investigations are carried out impartially, without pre-judgment. It would be inappropriate to comment further at this stage."