The agency overseeing the federal bureaucracy's workforce has told employers to prepare a "transition" back to office buildings for the thousands of staff working from home during the pandemic.

It also warned local outbreaks of COVID-19 could disrupt the return to workplaces and would need employers to be flexible about plans to phase out working-from-home arrangements.

The Australian Public Service Commission said there would be a "phased process" for agencies in transitioning their employees to their usual workplaces.

"Agency heads should develop and start to implement a transition plan to facilitate the transition of employees to usual workplaces," it said in a circular on Friday.

"In doing so, agency heads need to review the balance between working from home and returning to usual workplaces, ensuring the health and wellbeing of their staff along with agency productivity and the delivery of essential services."

Thousands of Commonwealth public servants, including 11,000 from the Australian Taxation Office, are working from home after a massive shift from the bureaucracy's workplaces in March.

The federal government's own "roadmap" to lifting COVID-19 restrictions signals that Australians working from home should stay there, if convenient for them and their employers, in the first two of the plan's three stages.

Agency heads will decide when federal public servants return to workplaces, however the public service commission said it published its new guidance to help them prepare for the transition.

It anticipates some bureaucrats will remain working from home for an extended period of time.

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In its circular, the commission said plans to return staff to workplaces should remain flexible and adapt to both local outbreaks of the coronavirus and changes in government advice about COVID-19 restrictions.

"The transition to usual workplaces may not be linear," the public service commission said.

"Where there is a localised outbreak, agency heads should facilitate Australian government employees in the location of the outbreak to work from home, where it is practicable to do so."

The commission said agencies shifting staff back to office buildings should consider prioritising employees with a greater need to be in the workplace.

Employers should also consider managing numbers of staff in workplaces where they cannot maintain physical distancing, including by rostering employees to work from the office or home on alternating days or weeks, or allowing more flexible start and finish times.

The public service commission said a single approach to returning public servants to workplaces was "not practicable" given the bureaucracy's diversity.

"Each agency's transition plans will be different and will be tailored to their particular circumstances," the circular said.

Community and Public Sector Union national secretary Melissa Donnelly warned public service employers against "jumping the gun" in shifting staff back to workplaces.

The move should be carefully mapped out, and take into account state and territory government advice, she said.

Public sector workers had genuine concerns about how health and safety measures, including social distancing, would be managed in APS workplaces, Ms Donnelly said.

"We know that in many buildings across the nation social distancing rules cannot be followed due to office fit outs and population," she said.

"That is why it is vital that concerns be properly addressed before widescale return to workplaces.

"Each of these steps are integral to avoiding the real potential of a second wave of COVID-19."

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