Changes to the bureaucracy's generous superannuation, seen as a "deal breaker" by many government workers have been taken off the table and the government's position on "productivity offsets" for pay deals appears to be softening.

But despite the concessions, the tough talk continued on Thursday from both public service minister Eric Abetz and his adversary, CPSU leader Nadine Flood.

Departments have been told they can back away from the demand that the Australian Public Service's generous 15.4 per cent superannuation guarantee be stripped from enterprise agreements before any deal could be signed.

It is understood that several departments have already moved to scrap the requirement with the Health Department's lead negotiator Adam Davey claiming in a announcement to staff that the move was consistent with previous positions.

There were signs on Wednesday that more concessions could be made to the government's hardline bargaining framework as the industrial unrest came home to Senator Abetz's own Employment Department and workers at the Tax Office made their first move toward strike action.

The Canberra Times revealed on Monday that superannuation guarantee had emerged as a major sticking point in the key Department of the Prime Minister and Cabinet, a position mirrored across the entire service.

The government wanted to strip the guarantee out of departmental enterprise agreements, arguing that the 15.4 per cent annual contribution, 6 per cent more than most workers receive, was protected in legislation and its presence in agreements is simply duplication and unnecessary red tape.

In January the Fair Work Commission backed the government, deciding there was no need to enshrine the guarantee into the new "modern award" for federal public servants and accepting Senator Abetz's argument that the super guarantee was already protected by legislation.

But the retirement-conscious Commonwealth workforce is not convinced and their main union the CPSU has achieved traction with its position that the move would leave the government free to try to get a cut, to the 9.5 per cent.

Public Service Commissioner John Lloyd advised chief negotiators of Commonwealth agencies on Wednesday they were no longer required to take the hard line on super.

It is also understood that departmental bosses may be allowed to seek "productivity offsets", a pre-condition for any pay rise offered, from areas of their budgets other than staffing.

That change of stance would allow bosses to relent in their attacks on conditions and entitlements, ending some of the stalemates that had developed and bring the possibility of deals closer.

But a spokesman for Senator Abetz played down the developments on Thursday afternoon that there had never been an issue over super.

"We said at the time that the PSSap superannuation clause in EBAs was of no practical consequence, therefore there is no issue with it being included," the spokesman said.

"I would urge the CPSU to be as flexible with its unsustainable 12.5% pay claim which will cost at least 10,000 jobs.

"They are more than aware that pay is not retrospective and the sooner they negotiate an agreement the better."

Ms Flood welcomed the development on superannuation but said the broader dispute was "far from over".

"This is a significant move because superannuation is such a critical issue," she said.

"Public servants were simply not prepared to give control of protecting their retirement income to Ministers Abetz and (Finance Minister) Mathias Cormann.

"This is a rare win for common-sense over ideology, but the CPSU's fight to protect other rights and conditions threatened by Minister Abetz's harsh bargaining regime is far from over. "

"Members will be keeping pressure on the government with escalating industrial action in many agencies."