They also frequently live in families suffering financial stress and compositional changes, while also having poor educational, social, and emotional outcomes.
The study by the Educational Research Centre found that a majority of children with special learning needs were not in receipt of educational or psychological supports.
It found that, overall, almost a fifth of all children aged 13 in Irish schools are classified as having special educational needs.
Based on data from the Growing UP in Ireland longitudinal study of more than 8,000 children, the study found that 17.9% of more than 7,500 children age 13 had some type of learning difficulty.
The report showed that more than a quarter of all the pupils had special education needs at either or both age 9 and age 13.
It also found that children with special needs adjusted less well to post-primary school, had poorer school attendance rates and were more likely to experience bullying.
The National Council for Special Education commissioned the report because it believed that, despite significant investment to support children with special educational needs over the past decade, there was only limited evidence in relation to the progress of these pupils and how they fare in school.
“There is a need for the development of structures and methods to enable early identification of and support for children with behavioural, emotional or social difficulties,” the report said.
It acknowledged that it represented a “challenging and complex task” for educational authorities.
The report welcomed the new model for allocating resources for pupils with special needs introduced in 2014 which, it said, was “fairer and more equitable” by having measures to take account of socio-economic disadvantage.
The study found a high proportion of children with special educational needs come from one-parent households (27.3%) compared to children without special educational needs (16.3%).
Out of the total number of pupils surveyed just under 9% had special educational needs at 9 but not at 13. Conversely approximately 7% of all children aged 13 were only identified as having special educational needs in the period since they were age 9.
The analysis found that 4.1% of all schoolchildren age 13 had behavioural, emotional, or social difficulties, with a slightly higher rate among girls than boys. It also revealed that 2.5% of all 13-year-olds had general learning disabilities or difficulties.