Danielle McMahon said she had seen her son Jay, 13, who has a variety of special needs including autism, take something off his head when she collected him off his regular special bus service home from his school last week.

Ms McMahon said her son told her that he and a couple of the other children were instructed by their bus driver to put the pillowcases over their heads and to "shut up and go to sleep".

Ms McMahon said she had been distressed to hear this and the family contacted the ACT Education Directorate which does not deliver the service directly, but contracts bus companies to provide transport for more than 470 children with special needs to a variety of schools across Canberra.

Ms McMahon said the directorate immediately contacted the company concerned and she was assured the driver would be sanctioned and all pillowcases would be removed from the bus.

A spokesman for the directorate confirmed that following the complaint being made "the bus company was contacted and took action to ensure the issue would not reoccur".

"The directorate takes all complaints about special needs transport seriously and works with families and transport companies to follow up on any issues brought to our attention," the spokesman said.

It was now "working to ensure that all special needs transport staff have completed disability awareness training. The ACT government is responsible for ensuring its drivers and attendants are appropriately trained, and has already made training arrangements for its special needs transport staff before the commencement of the new school year".

The manager of the bus company declined to comment on Wednesday but Ms McMahon was informed by the directorate that a different bus and driver would be assigned to Jay's bus route from Thursday onward.

"I am relieved that he no longer has to ride on a bus with a bus driver who clearly has issues dealing appropriately with vulnerable children but I am concerned about what this means for the other six kids who use that bus – none of whom are verbal," she said.

Ms McMahon noted that $17,416 out of Jay's National Disability Insurance Scheme funding this year was allocated to Special Needs Transport – specifically to fund his school bus service.

Ms McMahon said it was not the only complaint she had with the company and she had recently asked the directorate to request the driver not wear headphones while driving as they could not hear what children were doing during the bus trip.

"I don't fault the directorate in this, they are trying to contract out a service to get the kids to and from school, but I do think they need to make sure the drivers and aides are more sensitive to the kids' needs."

Ms McMahon, who worked for 13 years with vulnerable children through Barnardos, said she had heard the driver shout at the children and one time Jay had reported to her that he had been told to "change your underwear because you smell like shit" by a driver's aide.

"My son reports exactly what is said to him, he doesn't filter it, he doesn't lie."

Jay has a range of disabilities including hydrocephalus requiring two shunts in his head, a chronic bowel disorder requiring a port, eyesight and hearing problems and chronic lung disease.

He was born at just 25 weeks.

"They told me he would never walk or talk, but I took one look at him and fell in love," Ms McMahon said.

"I am just so proud of all the milestones that he has met."

She said parents of children with special needs needed assurances that government services contracted for their children would be held to strict account over their treatment whenever they were away from home.

"I literally can't be with Jay all day and I have to trust people to take care of him. With the bus service I really feel this trust has been broken."

The directorate spokesman said that the "other concerns are being worked through with the company to ensure the service provided is appropriate for the students and their families. Support has been offered and provided to the complainant. This will continue until the issue has been fully resolved".