But the government has two weeks to make its case before the HRC's decision is final.

It was thought the ruling could have ramifications for the Commonwealth Games timetable, which required the New Generation Rollingstock to be on the tracks.

But despite the findings, Queensland Rail will keep using the NGR for the Commonwealth Games timetable.

The trains have disability access issues, including the toilets and pathways being too small for wheelchairs.

Queensland Rail rolled out the first of the trains in December, despite the pending application to to the Human Rights Commission.

The HRC released its preliminary view on Friday, which it said gave parties an opportunity to respond before it made its final decision.

"The commission is of the preliminary view that it will refuse to grant the majority of the temporary exemptions sought by the applications in this matter," it wrote.

"Although the Queensland government has undertaken, within three years, to meet a legal obligation that has existed since the transport standards came into effect in 2002, the commission is not persuaded that the reasons advanced in favour of the exemption outweigh the discriminatory impact of the non-compliant trains on people with disability."

The HRC questioned why the then-Newman government bought non-compliant trains in the first place, and why the Palaszczuk government had not rectified the faults, saying the rules required all new trains to be compliant with the transport standards.

"It is not clear to the commission why the Queensland government procured non-compliant trains in 2013, or why the rectification work did not occur between procurement in 2013 and entry into passenger service in 2017," it wrote.

It would mean people with a disability had the right to bring a legal complaint under the Disability Discrimination Act.

Submissions are sought by March 16.

Inclusion Moves spokesman Geoff Trappett said the disability sector was heartened by the decision.

"The decision is one which will be a watershed moment for both Queensland Rail and the disability community, and I hope that many lessons will be learned," he said.

"The issue of legal action with the disability sector is something that is a matter for individual people with a disability to raise.

"The disability sector is, as it always has been, willing to work with the Department of Transport and Main Roads and Queensland Rail on inclusive transport."

The government applied for a temporary exemption for three years to allow it to progressively fix the non-compliance issues.

Queensland Rail chief executive Nick Easy has previously dodged questions on whether the NGR would be removed from service if the Human Rights Commission rejected the application.

Just this week, Transport Minister Mark Bailey revealed nine NGR trains were on the tracks, one more than was required to meet the Commonwealth Games timetable.

Ordered under the previous LNP government, the first NGR trains were due to be operational in mid-2016, but after the discovery of significant issues, including problems with braking, air-conditioning, sight lines for drivers and disability access, delivery was halted in March 2017.

Transport Minister Mark Bailey said the NGR trains would be on the tracks for the Commonwealth Games.

"We will be delivering the full transport plan for the Commonwealth Games, we will be working with the disability sector to work our way through these issues," he said.

Mr Bailey said the government look at the preliminary decision in detail and would make another submission.

It took 46 days between the close of submissions for the Commission to release its decision on March 2.

If it was to take another 46 days from the close of submissions on March 16, the final result would be announced on May 1, after the conclusion of the Commonwealth Games on April 15.