A survey of 146 class teachers in 20 schools, carried out by the Educational Institute of Scotland, shows that half are unhappy with the advice and information they receive.
Four out of 10 are unhappy with the number of specialist staff they are allocated while just over half are dissatified with the level of training.
More than six out of 10 want better support from the psychological service.
Frank Healy, local EIS secretary, said the survey reflected the frustration and anger teachers sometimes feel at not being able to meet the needs of every pupil.
"If mainstreaming is to work, it is essential that the levels of teacher dissatisfaction and other issues outlined in this survey are addressed in partnership with teachers and their professional associations. Only in this way will we be able to make the recommendations of the Audit Scotland report, Moving to Mainstream, a reality for all pupils and teachers in our schools," Mr Healy said.
The union's survey found that teachers are relatively content with how schools deploy non-teaching staff and monitor SEN pupils. They are least happy with consultation mechanisms.
Recurrent themes in the written responses from teachers include increased workload, support for inclusion as a policy but worries about lack of training for themselves and auxiliaries, and more time to discuss pupil needs.
There is strong support for smaller classes, restrictions on the number of SEN pupils and auxiliaries, and "more robust" prior assessment. There are also calls for pupils to have a designated auxiliary for a full day rather than half a day and for greater monitoring of auxiliaries' work.
A spokesman for East Dunbartonshire said that it was too early to respond in detail since the authority had just received a copy of the survey.
Three weeks ago, May Ferries, a prominent EIS member in Glasgow, said that while it was not politically correct to say inclusion was causing problems, "it is".