Bill Hughes, president of Work Wise - an organisation which has provided special needs training for more than 10 years - said: "Recent research findings suggest that existing special needs provision is not meeting the needs of either employers or the client group."
His organisation estimates that Pounds 22 million may have been wasted. "I am convinced that we have to alter our perspectives in terms of how we design and fund special needs training," he added.
Sir Donald Mackay, chairman of the jobs and training arm Scottish Enterprise, defended the organisation's commitment to special needs training. But, he admitted, "more effective targeting is needed to suit employers in particular".
Senior Work Wise staff claimed at a Glasgow conference last week that Scottish Enterprise's record was so unsatisfactory that it should cease to have sole responsibility for special needs training.
Work Wise chairman Roland Herman-Smith said: "If we don't get it right, then frankly we're wasting an awful lot of money."
Complaints were made at the conference that vocational qualifications got payment by results which prejudiced the chances of trainees with learning difficulties and disabilities.
Mr Hughes' comments were particularly embarrassing for ministers as he is credited with being the architect of the Scottish training and enterprise network.
The Work Wise philosophy is that special needs training, which covers 17 per cent of all those eligible for Government-funded training in Scotland, should focus more sharply on improving social skills and trainees' attitudes.
Caroline Farquhar, chief executive of Work Wise, urged Scottish Enterprise to emphasise personal development to help trainees become employable.
The research also highlighted wide variations in the definitions of special needs among the 13 local enterprise companies (equivalent to training and enterprise councils) which control training funds in central Scotland (the Highland network was not included in the study).
Few took account of ex-offenders or people with English as a second language. Glasgow is the only LEC which considers people with accommodation problems.