National Party member for Monaro John Barilaro says the department has taken a ''cookie-cutter'' approach in determining which NSW families get help transporting their children across the border to Canberra schools.

''One can't help but wonder what the departmental bureaucrats responsible for making these decisions would do if they had to swap places with people like [the mother] Janet and spend a day in her shoes,'' he said.

Janet and Nick Smith say the stress and exhaustion of raising two children with profound autism - Kye, 12, and Zac, nine, each non-verbal and incontinent - is being exacerbated by the battle with the department.

Mrs Smith says she has to run the gauntlet driving her sons between Queanbeyan and the Malkara School for children with disabilities in Garran because Kye routinely attacks her in the car, hitting her and pulling her hair.

Zac becomes extremely distressed by his brother's behaviour. If Mrs Smith has to pull over, that represents a break in routine for Zac who ''has a meltdown'', banging the window and escalating Kye's aggression towards his mother.

Malkara School has on four occasions been so worried about whether Mrs Smith will make it home safely that a staff member who also lives in Queanbeyan has followed behind in her own car.

Mrs Smith says the situation could be easily addressed because the department runs a bus for children with disabilities between Queanbeyan and special schools in Canberra. She has applied four times to access the bus for Zac through the department's Assisted School Travel Program but been knocked back each time over four years.

Mr Smith starts work at 7am so Mrs Smith has to drop her children at school before starting work in the library at Parliament House. Kye is due to start at a special needs high school next year which will mean two stops before getting to work. And all the while she is at risk of physical attack from Kye.

''I'm not a troublemaker. I feel they have backed me into a corner over this,'' she said, through tears. ''After four years, I don't know what else I can do.''

A departmental spokesman said the applications had been rejected because Mrs Smith had ''demonstrated capacity to transport her children as she works in Canberra and drives past the school on her way to work'' and ''both children attend a non-NSW school at the choice of the parent''.

He confirmed the department runs a bus service between NSW and the ACT but ''interstate transport is only offered in exceptional circumstances''. ''Applications for transport services in 2014 are currently being assessed. The capacity of a particular run will not be known until the assessment

process is complete,'' he said. Mrs Smith said the boys were in Canberra schools because they needed specialist care. Kye had been in a special unit at a Queanbeyan mainstream school but she believed it did not have the capacity to deal with his very high-level needs. He and Zac had been accepted into Malkara and she had seen an immediate improvement in their care.

''It was like a different planet,'' she said. ''The place is amazing. They've got the resources and the knowledge.''

Mrs Smith said she wanted Zac to travel on the department bus, which offered a door-to-door service and had a person other than the driver on board to supervise the children. At least then, she could focus on getting Kye to school safely without upsetting her younger son. Zac did not display the same aggression as Kye and would benefit from the social interaction of the bus, she said.

Mrs Smith said the fact her children had been accepted into Canberra special schools demonstrated they had high needs and should be where they would gain the greatest benefit. ''If there was an option in Queanbeyan, don't they think we would do it? I would rather have the kids in the car for five minutes, not 30 minutes. It's what the kids need,'' she said.

Mr Barilaro said he was approached by Mrs Smith for help. He was aware of other local families in a similar situation who had ''the good fortune to overcome these transport obstacles with the right sort of advice and assistance from care providers''.

''Sadly it would seem not every family emerges from this process with a positive outcome,'' he said. ''I accept that while all levels of government are working towards delivering a model for individual care packages that specifically address the needs of the person, it would appear that the Education Department continues to adopt a cookie-cutter approach when determining which family gets assistance.