The Tax Office and public sector union the CPSU will carry out a fresh round of consultation before Tax goes ahead with plans for its workplaces at Moonee Ponds in Victoria and Parramatta in Sydney's west after a conference in Fair Work Australia.

The restructure would see about 90 mid-level tax officials replaced by more junior staff.

The planned cuts come as the Tax Office is handed new powers this month to penalise breaches in the growing industry.

The Community and Public Sector Union has gone to Fair Work Australia to object to the plan.

The cuts affecting the monitoring of self-managed super funds were concentrated in the "superannuation active compliance" sections at Moonee Ponds and Parramatta.

But the restructure will have to wait after the commission's deputy president John Kovacic decided the two sides should go back to the negotiating table for more ''consultation''.

CPSU deputy president Alistair Waters said his union was happy with the outcome.

"We welcome this outcome in the commission," Mr Waters said.

"It is an important step in ensuring members get a real say on the changes that the ATO is proposing.

"The government is constantly telling us that we have a budget problem and yet it is cutting the very people who are bringing in the revenue."

A Tax Office spokeswoman said the office had approached the restructure in a fair and transparent way.

"We are confident that our processes are robust and that they will deliver a fair and transparent outcome for our staff," she said.

"We are continuing to work constructively with the CPSU on ensuring that we can resolve this matter as soon as possible."