Almost 12,000 children are officially classed as missing from school, a TES investigation has found.
The numbers have triggered growing concern for the "lost pupils", with children's charities and Ofsted inspectors warning they are at "serious risk" of physical, sexual and mental harm.
The statistics, obtained from every local authority using the Freedom of Information Act, show 11,911 pupils are missing from school, with large urban areas the worst offenders.
There are a number of reasons that children may be registered as "missing from education" - defined as those that have not had any kind of schooling for a month - including explanations as simple as being forced to wait for a school place after moving or being withheld from education by their parents.
But the new figures show the startling fact that nearly 1,500 children have completely dropped out of the system and cannot be traced.
Leicester has the highest number of children missing from education. Some 2,611 are not in school. Nine other local authorities - Birmingham, Kent, Bradford, Brent, Sheffield, Southampton, Doncaster and Westminster - each have more than 360 missing children. Some 69 local authorities claim to have none.
Every council is legally required to record the number of children in the area not in school, but there is no national system to help officers trace them or to share information with another local authority.
Former Barnardo's chief executive Martin Narey described the new total as "deeply troubling".
"School is somewhere that every child needs to be every day," he said. "For many of our most vulnerable young people it is the only stability they know, the only time when a little chaos is taken out of their lives, the only time when they are required to behave reasonably.
"It is the one place where poor life expectations can be reversed. So for thousands of children - inevitably those most in need of education - to be missing from school is deeply troubling. We need to keep children in school or, when removal is necessary, as it sometimes is, ensure alternative provision is always made available in a timely manner."
And Enver Solomon, policy director at the Children's Society, said: "It is vital children don't disappear from the school roll. There is a danger this could happen to vulnerable pupils if schools just focus on attainment and their welfare is overlooked.
"The most marginalised children have the most complex needs: they must be given additional help to remain in education."
The last official figures from the Government - made five years ago - estimated that there were 10,000 children missing from education.
A Department for Education spokeswoman said: "We expect local authorities to follow procedures to identify children in their area who may be out of school, ensure that these children are not missing out on their education, and allocate a place as quickly as possible."