Ofsted chief inspector Sir Michael Wilshaw has warned of “safeguarding issues” at Tower Hamlets and Birmingham schools that could lead to “potentially high numbers of pupils” disappearing from the system.

He was speaking after his teams visited schools in the so-called Trojan Horse affair in east London and Birmingham. In the Midlands, schools were infiltrated by hardline Muslim radicals while schools in east London have seen students fleeing the country to become “Jihadi brides” in Syria.

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In a letter to education secretary Nicky Morgan, the head of the schools watchdog said that schools had been removing pupils’ names from registers “without either the schools or the local authorities having an accurate understanding of where those pupils have gone”.

Reasons given by students include “gone to live with grandparents”, “moved to Manchester” and “gone back to Libya”. He said their fate was then unknown, making it difficult to assess whether the pupils were at risk from “extremist ideologies”. Their education could be continuing, for example, at unregistered schools.

Kadiza Sultana, Amira Abase and Shamima Begum - the three schoolgirls from Bethnal Green Academy
Kadiza Sultana, Amira Abase and Shamima Begum - the three schoolgirls from Bethnal Green Academy

A Department for Education spokesman said: “We will be taking immediate steps to strengthen our guidance to schools on safeguarding and to amend the current regulations about the information schools collect when a pupil is taken off the register.”

Sir Michael said the lack of legal requirement for schools to establish where their students had gone made it “very difficult, if not impossible” to establish if pupils were at risk.

He said: “We cannot be sure that some of the children whose destinations are unknown are not being exposed to harm, exploitation or the influence of extremist ideologies.”

A Department for Education spokesman said: “It is vital local authorities failing in this area take immediate action to establish the identities of children missing education and we are working with them to improve their approach so that children are kept safe from harm.”

The likely outcome of the intervention is that schools will be given clearer guidance on the gathering of more precise information about the future plans of pupils who have been taken off their registers.