The Doran Review found "tears arising from frustration and anger" were common in discussions with families about the education of their children.
It identifies examples of excellent practice, but is critical of the standard of education for some children with complex special needs.
One common issue identified was parents "having to repeat one's story over and over again" to different officials and meetings where key professionals simply failed to attend, or arrived with little knowledge of their child's needs.
The report found: "Some parents reported on meetings taking place and then the outcome being totally different from the decisions made at the time.
"A number of parents reported they were not listened to at the meetings and their opinions were ignored. Some children ... felt professionals often did not ask for their views or listen to them."
The report blames a lack of basic training for staff, allied to a poor understanding of how to meet pupils' needs.
It suggests a raft of reforms, including more training and a register of teachers with appropriate skills to ensure enough skilled staff are available.
In the early days of the Scottish Parliament, MSPs passed legislation designed to create a more inclusive society.
As a result, many more children with special needs go to mainstream schools instead of travelling to special schools.
In 2010, some 70,000 – or just over 10% of pupils in Scotland – were identified as having additional support needs. Of these, 63,000 were supported in mainstream schools.
However, while the intentions of the policy have been welcomed, there has been growing concern that insufficient resources and training are undermining it.
Peter Doran, the report's author, is supportive of inclusion, but said the recommendations would provide a focus for improvement beyond "buildings and expensive resources".
He said: "It is also about the expertise, values and attitudes that make a real difference to the experiences and outcomes for children and young people."
Dr Alasdair Allan, the Minister for Learning, also committed himself to inclusion.
He said the review "sets out a compelling vision and recommendations that will drive us forward".
He added: "The report emphasises the services that allow those opportunities to be accessed need to be inclusive, efficient, equitable and effective in meeting need.
"In addition, the presumption of mainstreaming remains, although we are clear, as reflected in the legislation, that for some children and young people their needs will be better met in specialist provision, rather than mainstream schools, and, where this is the case, that exception will continue to apply."
The Scottish Government-backed review concluded there was a lack of co-ordination and continuity across all services, such as health and education.
It made 21 recommendations calling for a more strategic approach to be taken in future, with services available wherever those who need them live in the country.
It also called for the Scottish Government to provide funding to nationally commissioned services to meet the complex additional support needs of children and young people and ensure the level of funding is not less than currently provided across the grant aided special schools.
Jackie Brock, chief executive of Children in Scotland, said the report identified much good practice. However, she praised Mr Doran for not "shying away" from the "current unacceptable shortfalls in service".
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