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Schools are required to follow "strict rules" on excluding pupils, a spokesman for the department of education said.
The spokeswoman suggested data exposing the thousands of autistic children excluded from school every year was not in line with Government policy on pupils with special needs.
Three out of every 10 parents with an autistic child in the UK have been asked to keep them at home, a disability charity has found.
Ambitious About Autism found of the 70,785 children who have autism:
- More than half of them were kept out of school by their parents who did not feel their child had the right support at school.
- One fifth (20%) had their child formally excluded from school in the last twelve months.
- Two fifths (40%) of parents had been asked to collect their child at an unscheduled time.
- The report also pointed out teachers were struggling with autistic pupils - 60% of educators felt they did not have enough training to deal with a student who had the disability.
Thousands of children with autism are being illegally excluded from school - partly because they are informally asked to leave the classroom for a few days - research has found.
Youngsters with the developmental disability are being asked to miss school trips, come to lessons part time or stay at home altogether, according to charity Ambitious about Autism.
Researchers from the charity spoke to 500 families, 1000 school staff and local councils to find how many autistic children were being excluded from school.
It found that four in 10 children with autism have been informally excluded from school temporarily - an illegal practice.
Jolanta Lasota, chief executive of Ambitious about Autism, said: "All schools are legally bound to provide quality full-time education to all pupils, including children with autism.
"Asking parents to collect their children early or putting them on part-time hours is against the law and fails to address the underlying need for schools to make reasonable adjustments to include children with autism."