An aide who allegedly told the 13-year-old boy to "change your underwear because you smell like shit" has also been stood down pending the outcome of an investigation into the incidents, a spokesman from the Education and Training Directorate confirmed.

Danielle McMahon, whose son Jay has a range of disabilities including autism, was distressed to hear 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" last week.

More than $17,000 of Jay's National Disability Insurance Scheme funding this year was allocated specifically to fund his school bus service.

The directorate said it contacted the transport provider on the day of the alleged incident and advised them to investigate the matter immediately.

"The directorate is continuing to work with the transport provider to ensure that students with special needs are transported safely and securely," a spokesman said.

The action comes as the ACT Council of Parents and Citizens Association calls for the ACT Education and Training Directorate to make disability awareness training for drivers and assistants on special needs buses mandatory.

The council has drafted a range of information sheets on understanding children with a disability as well as visual communication aids for drivers to have on hand to help them communicate with passengers.

"All of these drivers are coping as best as they can with situations that are far more difficult than most people can manage and sometimes they get it wrong," Libby Steeper, driver trainer and president of Friends of Brain Injured Children, said.

"We hope to give them more strategies so they're more likely to get it right."

Ms Steeper has provided training for ACTION and Keirs bus drivers in the past and said many drivers have welcomed it.

"There's quite a bit of expertise there, some of the drivers have been doing it for years and they're excellent. I was teaching granny to suck eggs with some them, but nevertheless, things change and you have to revise it and develop some new strategies.

"I don't want them to mistake a meltdown for instance for poor behaviour so they need a good understanding of those particular conditions then I give them some solutions on how to handle more difficult cases, for example a non-verbal child who's upset or a child having a seizure or bullying in buses."

Meanwhile a petition has been circulating calling on Keirs to install air-conditioning on its special needs buses.

Concerned parent Toni Minto said her daughter is getting off the bus "hot, sweating and lethargic".

"I'd even suggest that she is being exposed to brain damage due to the temperature on said bus," Ms Minto said.

She said surveys and testing had shown it to be detrimental to the health of children and animals being left in vehicles on hot days without sufficient air flow and cooling. "I endeavour to do everything in my power to help my daughter and other families in similar circumstance to be confident that our children's needs are met."

A spokesman from the directorate said it recently received a complaint about the lack of air-conditioning on one special needs transport bus.

"The majority of buses used by the provider are air-conditioned and all new buses that join the fleet are air-conditioned," he said.