The union says a patchwork of services has created a "serious inconsistency" across Scotland with no national strategy. "Parents of young people refer to the situation as a lottery," it states in its response to the Parliament's inquiry into special education.
Children in Scotland, which runs a national information and advice line, says "unacceptable inequalities" have arisen, often depending on where families live. A consultation meeting in Inverness revealed there were often too few staff to cope with assessments, review and delivery of services.
"Such circumstances can pose considerable problems for parents since many cannot access resources without a completed assessment, there is lack of redress and professional support for families who disagree with the assessment, and many children have to be sent outwith the authority to receive the services they are entitled to," it states.
Parents also complain that conditions such as Asperger's syndrome and autism tend not to be identified or given priority and that children with complex difficulties can find themselves without specialist services.
Children in Scotlandmaintains councils continue to have "differential practice" in recording children, particularly over those with social, emotional and behavioural difficulties, many of whom also have mental health problems.
The EIS urges ministers and local authorities to face up to the daily realities in schools of integration policies where support and training are frequently lacking. It lists 14 conditions if integration is to be effective. "If policies on integration are to succeed in the longer term, the Scottish Executive must face up to them," it warns.
The union adds: "If integration cannot be made to work, properly complemented by alternative provision where appropriate, then the social inclusion programme of both Westminster and the Scottish Executive will, at least in this area, be seen as a sham."
Children in Scotland believes barriers to inclusion in mainstream schools leave many pupils with "poor experiences". Parents and disability groups also complain that school admission rules discriminate against pupils with special educational needs.
On more technical matters, the EIS argues the preparation of records of needs can still be based on medical and related information. "Such an approach carries with it implications of deficiency which are outmoded and unacceptable to the EIS," it states.