"We quickly concluded that we had to do our own analysis on this," Bob Black revealed.
Mr Black was presenting evidence on the findings of the joint Audit Scotland and HM Inspectorate of Education report on mainstreaming, which follows recent legislation giving parents the automatic right to send their children to their local school and not to a special school.
Further legislation on access to buildings and the full curriculum for pupils with SEN also lay behind the investigation, which put the additional costs at between pound;38 million and pound;121 million a year.
Estimates suggest between 2,000 and 5,000 more children might transfer to their local school.
Mr Black described the findings as "a wake-up call to everyone involved in this", including education and health authorities, government ministers and officials, and the Scottish Parliament. Much more had to be done if the policies were to be implemented effectively. Resources would need to be available for accommodation, extra staffing and training but many authorities were unprepared.
The presumption of mainstreaming was attached to recent education legislation at a late stage and demanded "significant" resources that were not included in the proposals. "The financial memorandum was very short and rather vague," Mr Black warned.
Education ministers had argued that savings in the special school sector would offset the rise in the number of mainstreamed pupils.
Lesley Bloomer, the Audit Scotland official who headed the inquiry, reminded MSPs that there were no certainties in the costs since parents would decide where to educate their children. Special schools had to remain because of the opt-out clauses to mainstreaming.