Some schools put up barriers to stop parents from enrolling children with special needs, inspectors have claimed.
The first review of the system in 20 years has uncovered evidence of mothers and fathers being told another school would be more suitable or that the resources are not available for their child.
The National Council for Special Education (NCSE) warned that the fundamental need and right to enrolment was being ignored by some schools.
"This makes parents feel they have to fight for a placement and that their child is being enrolled on sufferance," its report found.
Inspectors said they were greatly concerned that regulations to ensure open enrolment for all are not in place. The NCSE said it had found evidence that some schools erect overt or soft barriers to prevent or discourage parents from enrolling children with special needs.
"We consider that schools are funded and resourced to provide an educational service to all children in their locality. Exclusionary practices cannot be permitted in any national system of education," it said.
Overall the NCSE, which spoke to pupils, parents, schools, teachers, health professionals and special needs assistants, said that children with special educational needs are being well supported in schools and making good progress. It said the education system offers 10,000 learning support and resource teachers, more than 630 special classes and more than 10,000 special needs assistants.
But on the issue of enrolment, its review found parents of children with special needs being encouraged to go elsewhere, to schools with more resources, and schools refusing to enrol children by claiming a lack of necessary resources, particularly in the health area.
It also identified schools that have refused to open a special class for a cohort of students, where a need has already been identified, where there is space and where additional resources can be made available.
The NCSE report stated that in 2011, 6,812 children were enrolled in special schools and 3,286 in special classes out of a total school population of 838,990.