Speaking at the Conservative Party Conference David Cameron said those teaching intolerance will be shut down.
"If an institution is teaching children intensively then whatever it's religion, we will, like any other school, make it register so it can be inspected - and be in no doubt, if you're teaching intolerance, we will shut you down," he said.
He promised the country that it was his "duty" to keep Britain safe and that it was time to "really confront extremism".
But the Evangelical Alliance warned any new measured had to be carefully considered.
David Landrum, director of advocacy at the Evangelical Alliance, said: "It is right that we actively 'rebuild Britain as an even greater country' and take stringent measures to eradicate extremist ideology.
"However, it is vital that committed Christians are not labelled as extremists by those who may disagree with aspects of their faith.
"Any bill to tackle extremism must not undermine the very democracy that it seeks to protect. We would urge the prime minister to consult with all faith groups to ensure that historic freedoms of religion and belief are secured in the implementation of this bill."
David Cameron added: "Did you know, in our country, there are some children who spend several hours each day at a madrassa?
"Let me be clear: there is nothing wrong with children learning about their faith, whether it's at madrassas, Sunday schools or Jewish yeshivas.
"But in some madrassas we've got children being taught that they shouldn't mix with people of other religions; being beaten; swallowing conspiracy theories about Jewish people.
"These children should be having their minds opened, their horizons broadened, not having their heads filled with poison and their hearts filled with hate."
He concluded: "So I can announce this today: If an institution is teaching children intensively, then whatever its religion, we will, like any other school, make it register so it can be inspected.
"And be in no doubt: if you are teaching intolerance, we will shut you down."
As part of his attempt to tackle the problem of extremism impacting young people, he has vowed to shut down Muslim Madrasas that preach hate to children, he added that schools "teaching children intensively" will have to register for inspection.
The PM stressed extremist schools were part of a wider problem of segregation within some communities, adding extreme madrassas "incubate these divisions".
"There are parts of Britain today where you can get by without ever speaking English or meeting anyone from another culture.
"For too long, we've been so frightened of causing offence that we haven't looked hard enough at what is going on in our communities.
"This is passive tolerance and I'll tell you where it leads: To children, British children, going to Pakistan in the summer holidays, before they've even started their GCSEs, and forced to marry a man they've never met."
"Children, British children, having their genitals mutilated, not just in a clinic in Lagos but the back streets in Britain.
"This passive tolerance has turned us into a less integrated country; it's put our children in danger. It is unforgivable.
"So let me say it right here: no more passive tolerance in Britain. We've passed the laws - now I want them enforced."
He also vowed to keep the nation safe, tackle poverty and ensure opportunities for all.
But Labour have criticised him for launching a personal attack on leader Jeremy Corybn.
