United Voice last year called on the ACT government to terminate the contracts of two companies which it accused of underpaying workers more than $500,000 over several years – a claim the companies have strenuously denied.

It also launched legal action against the companies – Phillips Cleaning Services and Rose Cleaning Service – in the federal court in an ongoing stoush over standards for Canberra's school cleaning contractors.

The two companies applied to the Fair Work Commission in June last year to scrap three rolling "clean start" enterprise agreements, which had promised higher pay rates and better conditions for the city's government-contracted cleaners.

The companies argued they had been disadvantaged because the pay rates outlined in those agreements were higher than the modern award, restricting their ability to get new work as they were not on "a level playing field" with competitors.

They said employees wouldn't be disadvantaged as they would continue to be paid the same rate until the contract was renewed, and argued scrapping the agreements was about employees' pay and conditions and did not affect the general public.

Rose Cleaning Service lodged petitions signed by 58 employees in support of two applications, as well as an audit of employees showing they had been paid correctly and treated fairly that was signed by 36 employees.

But United Voice, who opposed the bid, argued the employees would lose benefits they were entitled to under the existing agreements, which included some redundancy provisions, paid public holidays and four-hour minimum engagements.

They said in some cases migrant workers who didn't understand English didn't have those documents explained to them in a way they could understand, while others weren't given an opportunity to think about the petitions.

It also said terminating the agreements could encourage other employers covered by clean start agreements to also attempt to scrap their agreements.

In a decision published last month, commission deputy president John Kovacic ruled in favour of the union and dismissed the companies' applications.

He was not satisfied it was appropriate or in the public interest to terminate the agreements.

Mr Kovacic said while the petitions lodged by Rose Cleaning Service suggested that a majority of employees wanted the agreements to be scrapped, there was no evidence before the commission to back it up, meaning little weight could be attached to those documents.

"For instance, given the diverse ethnic backgrounds of the signatories to the petitions, no evidence was lead regarding whether or not employees were informed of the implications of termination, how that explanation was provided and whether or not they comprehended what those implications meant for them."

Ms Lyndal Ryan welcomed the decision and said it meant the union had been able to guard the employees' rights "this time".

"The union has succeeded in protecting those worker's rights and it's incredibly important for that group of workers to be protected by law."

Ms Ryan, who previously called on the ACT government to terminate the two cleaning companies' contracts, said the Canberra community would have expected a Labor government to stand up for workers' rights.

An ACT Education and Training Directorate spokeswoman said the government was aware of the union's concerns and the directorate would continue to investigate its claims to ensure all workers had access to fair and safe working conditions.