Parents of children with special needs are often asked to reduce the hours their children attend school, or take an extended break to avoid them being expelled altogether.
Disability advocates say this form of informal exclusion is common and parents often comply because they fear being left with no options.
For now, there is no disputes panel to oversee schools' decisions to expel children with special needs, but it is up to the school to place the student elsewhere.
A South Island-based mother of two, who RNZ agreed not to name, said her two autistic children spent only two hours at school each day because she worried that more time at school would lead to them behaving badly and being sent home for good.
"I'm taking that step before I'm pushed because I couldn't cope with the feelings that we are not wanted there so I voluntarily help the school out by not having them there."
She said her children had many behavioural problems but were highly intelligent, advanced learners.
"It's a difficult thing, there's no pressure to do it, but you know if they're there and something goes wrong that will be the end of school."
Her children have high needs and require more support than the education system will fund for them - but she believes mainstream schooling is important for their self-esteem as well as their education.
RNZ today reported that a 13-year-old autistic boy who was suspended after being involved in a fight had since been excluded from an Auckland school - despite appealing for help from the Children's Commissioner.
Equity in Education is a parent support and advocacy group for families with neuro-diverse children.
Spokesperson Frian Wadia said while formal suspensions were common, informal requests for the students to voluntarily take time off school were too.
"We hear a lot of stories where children are excluded. Not only are they formally excluded but there is a lot of informal exclusion as well, requests to stay home, requests to not come in for the next few weeks, those sorts of informal requests - it's rampant."
Wadia said some schools discouraged families with special needs children from enrolling.
"We know of families that have had to sell their houses just to get into a school zone where they find a more inclusive school so that is also something that is quite common. The sad part about that is we lose our community, we have to constantly move or look for something somewhere where our child will belong."
She would like to see more funding and resources for schools to cater to neuro-diverse students.
The Ministry of Education spends about $1.2 billion on learning support each year, and said it had employed an extra 180 ministry specialists and about 623 learning support coordinators over the last four years.
In a statement, Deputy Secretary Katrina Casey said the ministry would continue to work with families when young people had been excluded to make sure they could access education with the supports and resources they were entitled to.
Autism New Zealand chief executive Dane Dougan said exclusion was common but it was not the answer.
"We do hear many stories of schools excluding our community and also principals and both will exclude children until they get more funding and support," he said.
"We're still not resourcing the system well enough and we're not really providing enough training for the teachers and other educators in the school. It all starts from the top, so a lot of what we advocate for is making sure you get the principals on board to filter that culture down."
That resonated with the mother RNZ spoke to, who was concerned the current system was setting her children up to fail.
"It really would help if all staff had training in neuro-diversity, disability, mental health issues, across New Zealand where as it seems to be an optional thing for teachers to have that training."