Compensation will be offered to thousands of intellectually disabled workers, after a court ruled the system used to define their rate of pay was discriminatory.

One-off payments will be awarded to workers from government enterprises who can prove they have been financially disadvantaged by their low pay rates, which for some sat at just $4 per hour.

The payouts are the result of a recent court finding, after two men launched a case arguing they had been severely short-changed.

Gordon Prior and Michael Nojin were represented by lawyer Kairsty Wilson in their case before the Federal Court.

Ms Wilson says her clients were clearly getting the short end of the stick. She has also raised concerns that the ruling on a case currently still underway could make many thousand ineligible for the payments just offered.

“It's a pretty big catch, because at this stage the representative action catches all employees working at ADEs who have an intellectual disability and are assessed under BSWAT (Business Services Wages Assessment Tool),” she said.

“That's certainly what needs to be considered once we get a bit more information, and in discussion with Maurice Blackburn and the legal team that's involved in that.

“If you take Gordon Prior, when he was actually assessed under the supported wage system, there was a difference of $10 to $12 an hour,” Ms Wilson said.

“If you take that over a period of eight, nine years, that's a lot of money. One of our clients kept saying to me: ‘I want to be paid - I want to be able to go and buy groceries like other people can’.”

Australia's Disability Discrimination Commissioner, Graeme Innes says the pay-outs are a quick and cost-effective way to make sure the damage is reversed.

“The Government's saying: ‘Look, rather than go through the courts, we'll put a scheme in place to recompense people,” the commissioner said.

“I think it is a recognition or an acceptance by Government that discrimination has occurred, as determined by the Federal Court, and a recognition of the difficulty that people might experience in using the existing precedent to take legal action to recoup economic loss that they've experienced.”

“If the scheme is acceptable to the people involved, then it seems to me a much better process to have the money paid to people with disability than paid to lawyers,” Mr Innes said.