The 12-year-old has epilepsy and a chromosone condition so rare it doesn't have a name but it means she functions at the level of a six year old. Three years ago, her family thought they would lose her to a brain tumour. Now, she is about to graduate primary school.

But, after carefully-orchestrated plans to place Molly in a specialist learning unit at Melba Copland Secondary School abruptly fell through last week, her parents fear she will lag even further behind her peers in a mainstream classroom.

There are 48 learning support units across the territory's 107 schools, 14 of which are in high schools, where students with disabilities or autism can get more intensive support outside regular classes.

Molly's mother Rebecca Davey, who also chairs disability not-for-profit SHOUT, said she was explicitly told by the ACT education directorate the decision to deny Molly a spot in a unit came down to her postcode, not her needs.

The family live across the border in Murrumbateman but said they had been assured for the past three years they would not have to move to Canberra to guarantee her a place, as Molly's eligibility had already been ticked off.

In an email seen by The Canberra Times, the directorate later told the family the decision was based on the unit's capacity and Molly would still have a spot at the school with extra support.

A directorate spokesman said NSW students were given equal access to support units once they had been accepted into an ACT pathway school.

While places were based on the needs of students and the group, with extra resources provided where there was identified need, he also confirmed they hinged on the "location of the program in relation to where students live" and the unit's vacancies and capacities.

Students who could not get a place in support units were offered additional help in mainstream classrooms, the spokesman said.

In Molly's case, it is understood she will also have some access to the unit though the details are yet to be finalised. Ms Davey said the family had been left in limbo, back to where they started with a model that wasn't working for Molly.

A student's disability funding is given to schools to distribute based on need and Ms Davey said quieter kids like Molly were sometimes overlooked.

"She's not the kid throwing chairs around the room needing attention, when she's upset she tends to fall asleep, so her funding isn't always going to her needs," Ms Davey said.

The ACT government places a strong focus on supporting kids with disabilities in mainstream classes as part of its inclusion policy. But Molly's family say that, as she gets older, the arrangement is leaving her more isolated.

"When she was little it was easier for her to integrate but now she's an adolescent, she doesn't have friends. There's lovely kids who give her a hug, but she doesn't get invited to parties.

"She needs friends like her who still believe in Santa Claus and play with Peppa Pig figurines. She'll never catch up with the others.

"In a unit, she'll still be at school with her siblings, but she'll be able to learn what she really needs, life skills."

Specialist schools in the ACT such as Black Mountain School are also full at present. While the ACT is obliged to prioritise the enrolment of local students first, the spokesman did not say if this applied to enrolments of NSW students with disabilities, which are handled on a case-by-case basis.

Executive officer of advocacy group People with Disabilities ACT Robert Altamore said places in learning units should be determined by a child's need alone.

"There shouldn't be a cap," he said.

"There's a profound lack of co-ordination between NSW and the ACT and people with disabilities are having all kinds of cross-border issues."

The directorate did not say how a new limit on the number of schools in which NSW children can enrol affected students with disabilities.

Know more? Get in touch: sherryn.groch@fairfaxmedia.com.au