Vulnerable children could be at risk because of delays in compiling a national database to help co-ordination between child protection services.
Up to 10,000 children are 'missing' from UK schools
Lord Laming, who headed the Climbie Inquiry, fears another tragedy if gaps in the system are not closed.
His report into the death of eight-year-old Victoria Climbie from abuse and neglect led to a government promise to set up the system.
But problems over confidentiality and technology are stalling the project.
Lord Laming recommended that contact details should be kept for every child in the UK so that none would go "missing" from the system if they were kept out of school or healthcare.
A database could help services get the full picture of a child's needs but the two-year deadline set for the national scheme was missed this spring.
There have been objections from people who think the idea may breach children's civil liberties. Others claim that paedophiles could hack into the system.
'Hit and miss'
In East Sussex, one of the 15 councils asked to pilot the scheme, the east and west halves of the region disagreed on the type of system they wanted.
Project leader Lucy Ruddy told File On 4 she strongly felt the database was a good idea but it was difficult to ensure the information she had was accurate.
"We believe there are 135,000 children in East Sussex - but our current system holds about 180,000. I think we've counted a lot of children twice.
"We're looking at ways to have one gold standard of information about every child and young person so everybody can use it and at the moment they can't do that."
Despite this duplication, it was impossible to guess how many children were missing from the system altogether.
"I think there are an awful lot of children we don't know about and I think that's a disgrace.
"Areas we're concerned about are children where the families deliberately try to hide them, children who have recently moved into the county and have not accessed any service at all, transient children and recent immigrants with children who have a reason not to trust the authorities.
"It's absolutely the case that they may well be the most vulnerable children but as things stand at the moment it's extremely hit and miss whether anybody will ever find about them."
An estimated 10,000 pupils are missing from the UK's education system.
File On 4 looked at the case of a five year-old girl who was murdered after going missing.
The File On 4 programme hears from Danielle Reid's grandmother
Danielle Reid was taken out of her school in Inverness by her mother who told them she was moving to Manchester.
She was subsequently murdered by her mother's boyfriend and the couple dumped her body in the Caledonian Canal in a suitcase. It was not found for three months.
Highland Council has since introduced a system whereby schools must hear from an ex pupil's new school within 10 days or alert social services.
Its Director of Education, Bruce Robertson, said: "I think what this case demonstrated was that accepted practice across the UK was not adequate. The system had some pretty much fatal flaws and we needed to act swiftly."
In February this year, the then Children's Minister Margaret Hodge told a House of Commons committee that she had decided to set up a "universal" children's database, saying: "If you simply have a database of only those children that are at risk or in care, you have started to intervene too late."
However, Beverley Hughes, who replaced Mrs Hodge in May, told File On 4 that work was still being done to ensure the project was feasible in terms of cost and other criteria.
"Personally, I feel quite strongly the idea is a sound one and would add a great deal to the potential for us not to have communication breakdowns in the future - but I don't underestimate the range of problems that need to be overcome."
An announcement on the final decision over a database is expected in the autumn.
Lord Laming, who made his recommendation in January 2003, said it was essential it went ahead for better communication between child protection services.
"We need to ensure early signs are reacted to, and not wait until there is a disaster before people then come together and say 'If only I'd known'."
File On 4: BBC Radio 4, Tuesday 28 June, 2005 at 2000 BST, and repeated on Sunday 4 July, 2005 at 1700 BST.