Public servants at the Australian Taxation Office's Docklands and Gosford branches are saying goodbye to their personal workstations in a trial the Australian Services Union warns will end with staff adopting the trend nationally.

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

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

The ASU said Tax Office staff were not consulted about the trial, and has met with the ATO to try resolving the matter.

The union expects the dispute will go to the Fair Work Commission for arbitration and has vowed to take the fight to the tribunal.

ASU official Jeff Lapidos said the ATO previously said it was not planning to adopt hot-desking, but to the union's surprise, it announced in July it was trialling it in two offices anyway.

Mr Lapidos said Tax Commissioner Chris Jordan hadn't explained to staff why the agency was allowed to do this, but employees needed workstations set up for their workplace health needs to prevent injuries from repetitive movements.

ATO staff also wanted to put up photos of family to boost morale, something hot-desking offices stopped.

"All of those things make a difficult job more bearable," he said.

"It creates problems for people having to set up their own desks every day.

"It's a real robbery."

The dispute came as figures from the ATO showed it had slashed its number of vacant workstations in 2017 to 2300, or 9.71 per cent of its total desks, compared with 6700 or 24.7 per cent in 2014.

Mr Lapidos said the Tax Office wanted to make staff hot-desk to reduce its workstation numbers, despite a surplus of office space.

The ATO would not comment on its dispute with the ASU, but said its hot-desking trials conformed to "contemporary practices" and would make the agency more adaptable to business and staff needs.

"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 mobility, agility, collaboration and productivity," it said in a statement.

The Tax Office says it has cut its vacancy rate to its lowest on record, co-locating with the Department of Human Services and myGov in multiple cities, housing staff from other agencies in its buildings and subleasing its offices to other departments.

Offices with the most space are Penrith (19.39 per cent), Chermside (19.19) and Upper Mount Gravatt (15.45), while the tightest packed are Albury (1.52), Burnie (3.23) and Newcastle (3.92).

The ASU says the ATO is pushing hot-desking onto workers by exploiting a 2001 agreement to allow the trend to accommodate field staff helping introduce the GST.

ATO staff have resisted hot-desking in feedback to the union, saying the trial wasn't working as intended and that they lost time finding new desks.

Mr Lapidos said the union was waiting for documents promised by the Tax Office and which the ATO said proved it consulted with staff about the trial.