Many European countries continue to exclude disabled children, Roma children and migrants or refugees from mainstream schools, according to the report by the Council of Europe Commissioner for Human Rights.
"School segregation harms children's learning opportunities and is a clear injustice against minority and other vulnerable groups of people, which also perpetuates their marginalisation," said Nils Muiznieks.
Countries have an obligation to combat segregation in schools, but the reality is very different, the report said.
Political leaders and education authorities can sometimes be reluctant to bring about changes that alter the existing privilege in education, it added.
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"The legislation should be comprehensive and explicit enough to address situations in which tradition, freedom of choice, parental consent or urban segregation serve to legitimise discrimination and high concentrations of Roma children, children of migrant background or children with disabilities in specific schools," the report said.
A move towards more inclusive education systems will also require a change in attitude.
Parents of the majority population often prefer to send their children to schools without minority and migrant groups.