A study commissioned by the Department for Education and Skills found that many local authorities have little information on these children and have difficulty persuading schools to admit them if they are discovered.
Inspectors estimate the figure to be around 10,000 while the crime reduction charity Nacro believes it could be as high as 50,000. Concerns were heightened by the murder in 2000 of Victoria Climbie, who was not enrolled in a school.
In 2002 the DfES set a December 2005 deadline for every local authority to have "systematic arrangements in place" to identify missing children so that suitable provision could be made for them.
Researchers for the private consultancy Creative Research polled England's local authorities in March to check their progress. All 129 that responded had started putting systems in place, but many admitted they were "still at the early stages of bedding in".
Four out of 10 did not have a database of children not in education. Less than half had an agreed process for getting the children into schools and the data passed between schools was "patchy".
The DfES said the education bill due to be passed later this year would make it statutory for local authorities to have arrangements for finding the missing children.
"We are concerned, as it is not just their educational attainment which is at risk but also potentially their safety," a spokesman said.
Children missing education is at www.dfes.gov.uk