All councils are failing in their legal obligation to ensure the safety of every child who lives in their area, a report by inspectors warns.
The survey of 15 authorities by Ofsted, the education standards watchdog, revealed that not a single one was confident it knew of all the children living in its area.
In particular, it singled out independent schools and academies for failing to inform councils if a child disappeared or was taken off their roll.
"Children who become lost to the system not only risk failing academically but can be exposed to vulnerable situations," said Patrick Leeson, director for education and care at Ofsted.
"It is of serious concern that some schools are not following agreed procedures and legal requirements for notifying their local authorities when pupils are excluded or taken off the roll," the report states
It adds: "If their whereabouts then become unknown, they may be particularly at risk of physical, emotional and psychological harm."
Ofsted's fears come after several cases in which children have been withdrawn from school and subsequently suffered abuse at the hands of their parents or carers.
The inspectors warned that some children also go missing from school because their parents had arranged a forced marriage for them.
Lack of co-operation with other agencies such as the UK Border Agency can sometimes mean council officials are tied up for days searching for children who are no longer in the country.
"In one example given to inspectors, officers spent three days trying to trace a vulnerable child who had gone missing before they were informed that the child had been removed from the authority before being deported," said the report.
On private schools, they added: "Overall, there was little formal communication between the independent and state sectors about pupils' movements out of independent schools."
It also urged the Department for Education to persuade academies to liaise with council officials if they were excluding pupils or taking them off the roll.
"None of the children's services departments visited was confident that it was aware of all the children living in its area," it said.
"Officers in the authorities visited consistently said: 'We don't know what we don't know'."
In one authority, officials received 1,113 notifications from schools of children who were currently missing education. Six months later, it had still failed to track down 438 of them.
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