Children with special needs who have been excluded from schools for aggressive behaviour linked to their condition are being discriminated against, a judge has ruled.

Judge Alison Rowley, sitting in the upper tribunal, said it was “repugnant” to consider such behaviour as “criminal or antisocial” when it was a direct result of a child’s condition and “not a choice”.

The tribunal in London upheld an appeal involving a 13-year-old boy with special educational needs who had been excluded from school because of aggressive behaviour that was linked to his autism.

The ruling could affect tens of thousands of children who have conditions such as autism or attention deficit hyperactivity disorder (ADHD). Statistics show that children with special needs are at much higher risk than other children of being excluded from mainstream schools in England.

Noting that “aggressive behaviour is not a choice for children with autism”, Rowley found that a regulation under the Equality Act 2010 allowing schools to exclude disabled pupils for their behaviour without justification was unlawful and incompatible with human rights laws.

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“To my mind it is repugnant to define as ‘criminal or antisocial’ the effect of the behaviour of children whose condition (through no fault of their own) manifests itself in particular ways so as to justify treating them differently,” said Rowley.

The ruling – on an appeal brought by the boy’s parents and the National Autistic Society, and backed by Equality and Human Rights Commission – means exclusion decisions involving pupils with a “tendency to physical abuse” will no longer be exempt from the scope of equalities laws.

Jane Harris, of the National Autistic Society, said the verdict could transform the educational prospects of children on the autism spectrum, and she urged the government to ensure children were no longer being unfairly excluded.

“We intervened in this case to try to close a legal loophole which saw far too many children excluded from school. Before this judgment, schools were able to exclude pupils who have a ‘tendency to physical abuse’, even if the school had made no adjustments to meet their needs,” Harris said.

The parents of the boy, known as L, said they were delighted by the ruling. “School should be somewhere he can go without fear of discrimination or exclusion for actions which he has no control over. Knowing that one of the key rules that prevented that has now been found to be unlawful is of great comfort to us and, we hope, many other families,” they said.

Rowley said the current regulations came “nowhere near striking a fair balance between the rights of children such as L on the one side and the interests of the community on the other”.

But the judge also said schools should not be prevented from excluding pupils, provided it was a “proportionate response” and followed “reasonable adjustments” by the schools involved.

The Department for Education (DfE) said: “The government is fully committed to protecting the rights of children with disabilities as well as making sure schools are safe environments for all pupils. We will be carefully considering the judgment and its implications before deciding the next steps.”

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This year the DfE launched a review, led by the former MP Edward Timpson, looking at why some groups were disproportionately excluded by schools.

Paul Whiteman, general secretary of the National Association of Head Teachers, said schools were suffering from severe cuts to funding for special needs and disability provision and cuts to support services from local authorities.

“The decision to exclude a student is never taken lightly and always as a last resort. But school leaders do need the autonomy to decide when and how to exclude students to protect the health, safety, education or wellbeing of other pupils and staff in the school,” Whiteman said.

“Schools can’t do it on their own. To avoid exclusions they need support from the other local services around them. The issues that underpin exclusions reach far beyond the school gates, so schools need access to expert resources to help them support at an early stage those students who need more help.”