The Children's Commissioner has warned that a school's exclusion of an autistic boy is the tip of an iceberg of problems.

Judge Andrew Becroft intervened in the case after the boy, 13, wrote to him following his suspension for his involvement in a fight.

The boy moved to the school last year as a directed enrolment, meaning the Ministry of Education ordered the school to enrol him after it initially refused.

Becroft recently defended the rights of such children after the Principals' Federation suggested schools refuse to enrol them unless the ministry provided sufficient support to keep them and others safe.

The boy's letter, provided to RNZ by his mother, said his school would not let him participate in regular school activities and kept him in a room with a teacher away from but in full view of other children.

"I'm having a really hard time at school at the moment and hate being treated so differently to all the other students. I just want to make some friends and be treated like everyone else. I hate being bullied and laughed at because the teachers treat me differently and so do the other students," he wrote.

"Can you please come to my school and help me? I want to go to school and just be like everyone else. This is making me feel depressed and angry. Sometimes it makes me feel like I shouldn't exist."

After receiving the letter Becroft spoke to the boy's mother and to the school ahead of a board of trustees' hearing last week, which resolved to exclude the boy.

It was a complex case and the boy's mother and school had differing views of the situation, he said.

His office would remain involved.

"It's in no-one's interest to have a series of directed enrolments, it's certainly not in the interests of the young boy involved here. I think we want to ensure that this doesn't happen again in the best way we can and if that involves more resources and more involvement, absolutely so be it," he said.

"All children have a place in school. That's where children flourish best and we want to avoid having to segregate children who are neuro-diverse or challenging."

The case highlighted the urgent need for an appeal process so families could challenge school decisions that might have a lasting impact on children's futures, Becroft said.

"For this mother there's effectively nowhere to go that isn't super expensive or very long-term involvement ... to get a quick appeal, second-look at the decision," he said.

"There are hundreds of independent boards making these decisions without any second look or necessary consistency and that's without in any way criticising the board involved at all. It's the only form of decision-making I know in New Zealand that is somehow exempt from an appeal process or a review process.

"How can we have a system that just strikes right at the heart of children's futures where there's no appeal?"

Becroft said it was clear from the volume of complaints that his office received that schools did not receive enough support for children with challenging behaviour.

The boy's mother, who RNZ agreed not to name in order to protect the boy's identity, said she was taking legal advice and was unsure if she would appeal the school's decision.

The school suspended her son because he retaliated after an older boy from a nearby school punched him in the head, she said.

The school's board was wrong to exclude him, she said.

"It's hugely disappointing, it's frustrating, it's beyond belief when you come with a positive solutions-based approach to getting the best education for your child, supporting not only the child but the school and they refuse to accept it, they don't want to know."

She had heard principals complain that they needed more support when they were ordered to enrol children with challenging behaviour.

But her son received one of the highest possible levels of support through the High and Complex Needs system and the real problem was the school's failure to make changes that included her son, she said.

Her son wrote to the Children's Commissioner because he wanted someone with authority to listen to him.

"He basically feels like a second-class person in a world that hates him because he's not been given a chance to prove himself."

Her son had previously been excluded from other schools, she said.

The school's principal refused to comment.

-RNZ/John Gerritsen.