The Fair Work Commission in Melbourne will hear the dispute over the ATO's plans to follow the controversial hot-desking trend, which the agency says will help it use space more efficiently.

Hot-desking has met firm resistance from the two unions representing Tax Office staff, which argue the agency cannot adopt the office fit-outs for all employees under its industrial agreement.

The Australian Services Union and Community and Public Sector Union will argue on Thursday the workplace deal only allows the ATO to require staff doing fieldwork to share desks.

Hot-desking - an office plan where staff find a new desk each day and pack their work into lockers before going home - has been widely adopted in the private sector by firms hoping to reduce wasted space and build teamwork.

But the trend has caused frustration for many employees who say it disrupts their work and poses health and safety problems.

An ATO spokeswoman said it had no plans to convert all offices to the new design, but where it could fit out new buildings or refurbish them, it would "consider how to design spaces in a way that creates a healthy working environment that improves flexibility, agility, collaboration and productivity."

The ATO has trialled "activity-based working" at Docklands and plans to adopt it more permanently, and to introduce it at the agency's new office in Gosford.

The Tax Office's spokeswoman said on Wednesday that feedback it received from its trials through an independent evaluation revealed overwhelming support, and that staff were lining up to work in the new office layout.

"Our staff working in this environment have told us they have spent more time sharing their ideas and knowledge and believe they have increased their individual and team productivity," she said.

ASU official Jeff Lapidos said ATO staff were opposed to hot-desking, and that those who participated in the trial were self-selecting and were able to opt out if they didn't like it.

The trial also used an office plan that featured luxurious, open spaces and places to relax and have meals, but was unlikely to be adopted in practice, he said.