Up to 100,000 pupils, or six times the number with records of need, could qualify for a co-ordinated support plan (CSP), MSPs were warned on Wednesday.
A major rift has surfaced between the Convention of Scottish Local Authorities and the Scottish Executive over the likely costs as Holyrood's education, culture and sport committee continues to take evidence on the additional support for learning Bill.
Tensions are rising because of pressure from Audit Scotland, the public spending watchdog, to ensure that education Bills are properly costed after the failure of previous legislation on mainstreaming pupils to put accurate figures against likely numbers who will be educated in their local school and not in special schools and units.
The new Bill replaces special educational needs (SEN) with additional support needs (ASN) but has not avoided the same argument over numbers and costs. Executive officials last week suggested that only a little over half of those with records of need (some 17,000) were likely to gain a CSP.
Around 2.3 per cent of the school population has a record.
Ewan Aitken, Cosla's education spokesman, dismissed Executive estimates this week while agreeing that none of the parties involved had a clear handle on numbers and costs because of the different system outlined in the Bill.
Mr Aitken says that up to 15 per cent of the school population may qualify for a support plan, way beyond conservative estimates in the Bill. Cosla advisers point out that the Warnock report 20 years ago suggested that up to a quarter of pupils had particular needs.
To gain a CSP, pupils must have had complex needs for more than a year which involve agencies outside education or in a different part of the local authority.
Mr Aitken warned: "The Bill is in danger of creating a three-tier system of children and young people without any intervention, those with ASN but without a co-ordinated support plan, and those with a co-ordinated support plan."
Young people were at risk of further labelling that the new system was designed to alleviate.
He feared there would be "huge resource implications". It was not so much that the Executive's figures were wrong, more that the full details had yet to be worked out. Cosla is working up its own costs and the sums are likely to be many times higher than those from the Executive.
In a written submission to MSPs, the authorities stress the sharply rising costs of SEN with a 15 per cent increase over the past two years. "This trend is likely to continue or even accelerate under the ASL (additional support for learning) system," it cautions.