Schools are being used by individuals who want to narrow youngsters' horizons, and in the worst cases "indoctrinate impressionable minds" under the guise of religious belief, the head of Ofsted is warning.
Inspectors are increasingly coming across those who want to "actively pervert" the purpose of education, according to Amanda Spielman.
In a speech on Thursday, she will warn schools that they should not assume that the "most conservative voices" of a particular faith group speak for everyone, and that they must not be afraid to "call out" any practices that they feel could have a negative impact on young people.
She will also offer her support to the headteacher of a school that was forced to back down over plans to ban young pupils from wearing the hijab in class, saying school leaders have the right to set uniform rules "as they see fit".
Ms Spielman will tell a Church of England education conference in central London that while many faith schools are good at promoting tolerance of religions, lifestyles and cultures, there is a difference between showing tolerance and respect for others and "privileging all belief above criticism."
"Ofsted inspectors are increasingly brought into contact with those who want to actively pervert the purpose of education," she will say.
"Under the pretext of religious belief, they use education institutions, legal and illegal, to narrow young people's horizons, to isolate and segregate, and in the worst cases to indoctrinate impressionable minds with extremist ideology.
"Freedom of belief in the private sphere is paramount, but in our schools it is our responsibility to tackle those who actively undermine fundamental British values or equalities law.
"That doesn't just mean Ofsted, but everyone involved in education. Rather than adopting a passive liberalism, that says 'anything goes' for fear of causing offence, schools leaders should be promoting a muscular liberalism.
"That sort of liberalism holds no truck for ideologies that seek to close minds or narrow opportunity.
"Occasionally that will mean taking uncomfortable decisions or having tough conversations. It means not assuming that the most conservative voices in a particular faith speak for everyone - imagine if people thought the Christian Institute were the sole voice of Anglicanism. And it means schools must not be afraid, to call out practices, whatever their justification, that limit young people's experiences and learning in school.
"In that regard schools must not, in their entirely correct goal of promoting tolerance, shy away from challenging fundamentalist practice where it appears in their schools or communities.
"Similarly schools must not allow pressure from certain elements of school communities to dictate school policy, nor should we allow vocal parental minorities to pressure other parents and children to act or dress against their wishes. Giving way to the loudest voices is the opposite of tolerance."
The chief inspector will also say that the schools' watchdog will "always back heads who take decisions in their interests of their pupils", as she offers her support to the head of St Stephen's primary school in east London, which hit the headlines earlier this month after it emerged it planned to block pupils aged under eight from wearing the hijab in the classroom.
The school faced a severe backlash for the decision, which was later reversed.
Offering her support to St Stephen's headteacher, Neena Lall, Ms Spielman will say: "School leaders must have the right to set school uniform policies in a way that they see fit, in order to promote cohesion.
"It is a matter of deep regret that this outstanding school has been subject to a campaign of abuse by some elements within the community.
"I want to be absolutely clear, Ofsted will always back heads who take tough decisions in the interests of their pupils."