The survey of 1,100 schools, carried out by the National Confederation of Parent-Teacher Associations, also found that more than two-thirds of secondary schools said they had problems with overcrowding in specialist teaching areas.
Many primary staff lacked confidence in teaching the national curriculum - especially in music, design technology and information technology - and parents were finding it increasingly difficult to raise funds for schools. The reasons given were unemployment and the realisation that the shortfalls could not be funded in a sustained way.
The confederation said that the picture presented by the initial results of the survey was "very depressing".
The code of practice, brought in under the 1993 Education Act, provides a framework for standardising procedures in schools dealing with children with special needs.
Schools are now expected to appoint a special needs co-ordinator and link up with local authorities and other agencies. They are also required to monitor children with special needs and keep systematic records.
Sixty per cent of primary and secondary schools said they found it difficult to meet the requirements of the code within their budgets. The confederation calls for a national review of the code of practice to identify the major areas of concern and the provision of non-contact time for teachers in monitoring and evaluation programmes. It calls for extra in-service training and targeted funding in school budgets for special needs.
Sandi Marshall, a member of the confederation's research and publications committee and one of the authors of the report, said "The survey confirms our worst fears about under-resourcing in schools.
"From a parent's point of view it is very worrying. If teachers are not getting the training they need there's more chance that a child with special needs will slip through the net."
The confederation calls for imp-roved initial and in-service training for teachers and a slimmer national curriculum at key stage 2.