A stoush between unions and the Australian Taxation Office went to the Fair Work Commission, which heard arguments the agency was prohibited from adopting hot-desking for non-fieldwork staff by its new industrial deal.

In a decision on Wednesday, Fair Work found the agreement let the ATO move all of its public servants into hot-desking, an office set-up whereby staff find new desks each day and pack up their belongings before finishing.

But the Tax Office, which wants to adopt hot-desking at its new Gosford office and has trialled it at Docklands, said it had no plans to roll it out in all workplaces.

"Where there is the opportunity in the fit-out of new buildings or refurbishments the ATO will consider how to design spaces in a way that creates a healthy working environment that improves flexibility, agility, collaboration and productivity," a spokeswoman said.

Australian Services Union official Jeff Lapidos said the decision was disappointing and that it would review the finding to see if there was any grounds for appeal.

The union would meet with the ATO in January about hot-desking, and was not happy with the fit-out of the Gosford office where desks were too small and lockers too far from workstations, he said.

The Community and Public Sector Union said the hot-desking matter had not ended.

CPSU ATO national organiser Matthew Harrison said it was far from convinced that hot-desking was a smart or cost-effective way to organise workplaces.

"There's plenty of research out there to back us up on our concerns about its impact on the morale and well-being of workers as well as productivity," he said.

"Our priority now is to ensure the use of hot-desking at these two trial sites causes the minimum possible disruption, and that any future decisions on hot-desking at other sites are made after proper consultation and after properly considering all the facts."

The ASU told Fair Work at a hearing last month that ATO staff believed they were backing a workplace deal that would stop bosses rolling out hot-desking when they voted up a new enterprise agreement this year.

A CPSU representative also said while the Tax Office had been open about its wish to introduce hot-desking, unions were clear they opposed it in negotiations.

The unions argued the workplace deal only allowed the Tax Office to require staff doing fieldwork to share desks, a point that Fair Work vice president Joseph Catanzariti disagreed with.

He also rejected union arguments that the ATO during negotiations of the new workplace deal had apparently not intended to introduce hot-desking afterwards.

"The evidence presented at the hearing clearly demonstrates that ATO employees were aware that the ATO intended on utilising shared accommodation," he said.