Deputy commissioner and acting chief operating officer Bradley Chapman told the court on Wednesday that a guide to working from home rolled out in March 2020 was a response to the emergency situation caused by the onset of COVID.

However a union representative for ATO staff said the agency misled him about its approach to pandemic-related working from home arrangements.

The Tax Office is defending against allegations from the Australian Services Union that the agency breached workplace laws by calling staff back to the office during the pandemic without the notice periods required under the agency's enterprise agreement.

Mr Chapman told the Federal Court hearing in Melbourne that the work from home guide it published in March 2020 was unrelated to parts of the agency's enterprise agreement dealing with remote working.

"This is about an emergency interim working from home guide," he said.

"The very language that was used was trying to make sure that that was clear, that this was an emergency response, not something that would persist as an ongoing arrangement."

Mr Chapman said the ATO was surprised when it saw the ASU describe the COVID-related work-from-home arrangements it established with staff as formal arrangements under the enterprise agreement.

The arrangements were instead intended to deal with the pandemic, he said.

"At that point in time we did not understand yet whether there would be blanket shutdowns where we may not have a choice as to having people in the office at all," Mr Chapman said.

"So that is very much about how we maximise the clarity of providing people with guidance as to what they should do in order to be able to transition to working from home immediately, in the event that their site is shut down."

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A later version of the ATO's work from home guide mentioned a review date after the agency's senior officials decided to clarify that the arrangements were an emergency response to COVID, Mr Chapman said.

"It was not our new normal way of working, and therefore we didn't want to set the expectation that forevermore, this is the way things would be so we needed to ensure that there were review dates but also we knew that with the changing environment people's circumstances would change so we'd need to make sure these things remained current."

The ATO told staff returning to the office after the height of the pandemic that they could access working-from-home arrangements under the enterprise agreements, if they wanted to keep remote working for part of the week and where it was suitable to them and their team, Mr Chapman said.

The ASU's lodged an application to the Federal Court to find the Commonwealth, the ATO and four of its senior executives breached the Fair Work Act in the way they organised its COVID-19 working from home arrangements between March and July 2020.

ASU official Jeff Lapidos, who represents ATO staff, said the agency had misled the union in March 2020 about its approach to moving staff to working from home arrangements.

The union was not aware that the Tax Office did not consider its COVID-related work-from-home arrangements were unrelated to remote working under the enterprise agreement.

Mr Lapidos said if he had known, he would have advised ATO workers to insist on having working from arrangements under the enterprise agreement, not the Tax Office's COVID-related remote working arrangements.

"My attitude to the whole thing and what the union would have done, if it had been drawn to our attention, is completely different to the position we took at the time," he said.

"We were being trying to be helpful and cooperative with the office, with them introducing these things. And it was done under false pretences from my perspective."

The hearing continues.