The Education Secretary, Nicky Morgan, has asked officials to review home schooling amid fears that thousand of children are having their minds “filled with poison” by radicalised parents.

Between 20,000 and 50,000 children are thought to be educated at home – but the Government has no idea of the exact number because parents are under no obligation to inform their local council.

Ms Morgan has already announced a crackdown on unregistered schools and “weekend madrassas” after some were found to be promoting extremist ideology. But senior government sources have revealed that home schooling is now “on the radar”.

Under proposals being considered in Whitehall, parents and teachers will be given a specific point of contact at local councils in order to raise concerns about a child. Officials will also try to discover how many children are being taught at home, beyond the reach of inspectors.

A senior government source said: “There has always been the freedom in this country for people to educate their children at home. Many people do it very well. But we need to know where the children are and to be certain that they are safe. For every parent doing a brilliant job, there may be someone filling their child’s mind with poison. We just don’t know. We don’t have reliable figures.”

The focus on home schooling highlights growing concern in government over the problem of children being radicalised by religious extremists abusing positions of trust to promote hardline doctrine.

Fears have been raised that parents are claiming their children are being home schooled when in fact they are being taught at illegal religious schools. Ofsted’s chief schools inspector, Sir Michael Wilshaw, has warned of the “serious and growing threat” to the safety of children posed by unregistered Islamic education centres.

A Department for Education spokesman said Ms Morgan was “determined to tackle radicalisation wherever it occurs”.

He said: “We have provided Ofsted with extra inspectors to eradicate extremism in education. We are working with them to address their concerns about home education being exploited, while safeguarding the rights of parents to determine how and where to educate their children.”

Under the last Labour Government, Ed Balls – as minister for children and families – commissioned a review into home education. However, a recommendation to set up a voluntary registration scheme for parents who chose to teach their children at home had to be abandoned because it was not supported by the Tories ahead of the election.

The new Conservative chairman of the Education Select Committee, Neil Carmichael, has endorsed proposals for more safeguards for children educated at home. He told the Tory party conference in October: “I find it absolutely amazing people who are home educated are not registered as being home educated. It’s an absolute scandal that should not be allowed.”

Nicky Morgan has tabled an amendment to the legislation ensuring academies can also be “held to account” and subjected to “robust action” (Rex)

But the Conservative MP Graham Stuart, who chairs the all-party parliamentary group on home education, said the Government should not even consider a register of home-schooled children.

He said: “The home is used by parents to inculcate ideas into their children’s heads all the time. Just because there is a problem does not mean there can be a solution.

“If the next step is a formal register I would resist that strongly. The legal duty to educate a child rests with the parents, not the state. That is a long-standing settlement in this country.”

Currently, only parents whose children have been offered a place in school have to inform a school’s head teacher if they then decide the educate them at home. If not, there is no obligation for a parent to inform anyone.

According to Department for Education advice, if a local authority has concerns it can make an “informal enquiry” to make sure the child is getting a suitable education.

Speaking to The Independent on Sunday, Fiona Nicholson, of the Home Education Consultancy, said: “Any investigation would lead me to suspect they are going down the route of compulsory registration for parents to have to tell somebody that this is what they are doing. I’m against that – you can’t separate it from having to ask permission.

“You can disagree with lots of ways parents bring up their children but until a crime has been committed, or there is a substantial child-protection issue, I don’t think it’s anybody’s business. It’s more than a slippery slope, it’s off a precipice really.”

However, Labour’s shadow Education Secretary, Lucy Powell, said the inability of authorities to know how many children were being home schooled was a “worrying weak spot for Government”.

She said: “It is vital that action is taken to ensure that all children, whether in school or taught at home, are given the knowledge and skills to succeed, not taught a narrow curriculum of hate and bigotry. Yet, just last week it was revealed that the Government had let children remain in illegal, unregistered schools for weeks, where they were exposed to narrow curriculums, misogynist, homophobic and anti-Semitic material. This is completely unacceptable.”