The engines will remain on the tracks for the near future, but the ruling provides ammunition for complaints and legal action being threatened by disability groups, with the latter having the potential to put the trains out of action through a Federal Court injunction.

The HRC decision was published on Thursday and rejected most of the exemptions proposed by the State Government and Queensland Rail.

Only one exemption was granted, cutting QR some slack with regards to ensuring an assisted boarding device was available at all stations.

The application for the NGR trains to be exempt from disability access laws was lodged on the basis that the engines were crucial to the Commonwealth Games travel plans.

"The Commission acknowledges that the Queensland Government has agreed to allocate funds to bring the trains into substantial compliance with the Transport Standards within three years," the Human Rights Commision said in a summary of its decision.

"The Commission is not convinced that this commitment is sufficiently persuasive to suspend the rights of people who might experience discrimination on the NGR trains during this time to make a complaint under the Disability Discrimination Act.

"In forming its decision, the Commission considered the views contained in 20 submissions received from individuals, government agencies and disability advocacy organisations.

"The majority of these submissions opposed the Commission granting the exemptions to the applicants, either outright or on the conditions requested by the applicants."

Wendy Lovelace, a Brisbane architect who uses a wheelchair and advises on improving access for people living with disabilities, has threatened to impose a Federal Court injunction.

She told Fairfax Media on Thursday that she was continuing to receive legal advice on her plans to take the trains off the tracks.

"The decision highlights that the government has done the wrong thing by putting non-compliant trains into service," Ms Lovelace said.

"They needed to have consultations and fix the trains appropriately before putting them into service.

"The outcome highlights the concerns held by the disability sector for some years."

Transport Minister Mark Bailey said the Palaszczuk Government "deeply regrets" the errors made with regards to the NGR trains, but was adamant the engines would be running during the Commonwealth Games.

"Today’s decision does not prohibit NGR trains from operating in passenger service, but does allow for complaints to be made on this issue," he said.

"Queenslanders and visitors can be assured that the Commonwealth Games transport plan, including the 24/7 rail timetable on the Gold Coast line, will operate as planned.

"The Palaszczuk Government is fixing the trains. We are committed to working with the disability sector to fix the trains as soon as possible."