Increased inclusion in mainstream classes could add almost a third to council's budgets for Special Educational Needs, if estimates of another 2000-5000 pupils prove correct. Special school numbers are predicted to fall from 8,000 to between 3,000 and 6,000 - resulting in further closures.
A joint Audit Scotland and HMI report into the controversial policy has warned MSPs that anything from pound;38-pound;121 million extra a year will have to be found. Special education accounts for around 9 per cent of councils' total spending on education.
On average, authorities estimate that every primary will have one more SEN pupil and every secondary four to five as schools become better equipped to cope and as the policy becomes more popular with parents.
Currently nearly two out of three SEN pupils - some 30,000 - attend their local school, while the remaining 14,000 are split evenly between special schools and units attached to mainstream schools. One pupil in every 20 has been classed as having special needs.
Existing spending runs to about pound;388 million and this is bound to rise when the statutory "presumption of mainstreaming" takes effect in August.
In a frank assessment, Audit Scotland says that planning for this change is "patchy in councils and minimal in NHS bodies". The majority of pupils will have moderate learning difficulties and the most significant impact is likely to be in larger urban councils which make the most use of special schools. Glasgow is the largest user.
Audit Scotland states: "Even the most successful schools had not been able to meet fully the particular needs of one or more pupils."
Alastair MacNeish, chairman of the Accounts Commission, the public spending watchdog, said: "Mainstreaming has been proven to work well but only when pupils and teachers are properly supported. Councils and NHS bodies need to gear up for this change by making sure school buildings are adapted, staff trained and therapy services can cope."
"Moving to mainstream: the inclusion of pupils with special educational needs in mainstream schools" is published by Audit Scotland and HM Inspectorate of Education.