Education watchdog Ofsted has said Luton is an “area of concern” over missing children at risk of radicalisation.
Ofsted boss Sir Michael Wilshaw singled out Luton, Bradford and Birmingham who he said were failing to support headteachers .
He said work to protect children would be a “waste of time” if the councils do not improve the tracking of pupils who leave mainstream educationd.
He warned that missing pupils could be at risk of exposure to extremism, saying headteachers felt “unsupported”.
In Birmingham more than 250 children had been removed from a council register without being located.
His comments come after he wrote to Education Secretary Nicky Morgan to raise the issue, two years after the Trojan Horse scandal in the West Midlands city.
Sir Michael told the BBC: “Our concern at Ofsted, my concern as chief inspector, is these children could be in unregistered schools, they could be in illegal schools, they could be vulnerable to all sorts of influences including radical and extremist thoughts.
“We need to know where these youngsters are.
“It’s not impossible - this is the duty of a local authority. They have, enshrined in statute, safeguarding responsibilities for all children no matter which institution they go to.
“They should commit resources to this and track this - otherwise all the work we do to get schools to promote British values, all the work Ofsted does to ensure children’s safeguarding will be a bit of a waste of time if there are significant numbers of children that are outside mainstream provision.”
In a newly published letter, the Ofsted Chief Inspector said he has continuing concerns about the performance of Birmingham City Council and its ability to protect and ensure the safety of its children.
In 2014, the city found itself at the centre of the so-called Trojan Horse controversy, which centred on an alleged move by a small group of hard-line Muslims to seize control of a small number of the city’s schools.
Sir Michael concludes that some of the “serious shortcomings” he outlines are not confirmed to Birmingham City Council and that he is worried about the ability of a number of authorities to address risks intheir area.
He added: “I have recently visited both Bradford and Luton to learn more about the level and quality of safeguarding in these areas.”
“From my meetings with senior officials and elected councillors from both local authorities, it was clear that much more needs to be done to ensure that the possible risks to certain groups of children are fully understood and acted on.”
Sir Michael calls on Mrs Morgan to agree for an Ofsted inspector to be assigned to any local authority where the Government considers that children “are at a greater risk of radicalisation or their safety is being put in jeopardy by poor safeguarding practices”.