Departments have signalled they see little point in further negotiation with unions in light of the instructions from government to stick to the hardline Abbott-era bargaining policy, and are now pushing for ballots to try to get their public servants to finally accept the deals on offer.

The news comes as the public service authorities claim the tide in the three-year dispute is turning in their favour, with about 250 public sector workers in four agencies accepting new pay deals since the election.

About 100,000 public servants are still holding out against the workplace deals they have been offered in a dispute that is now in its third year while about 50,000 federal government workers have agreed to sign up to new enterprise agreements offered under the bargaining policy.

Public Service Minister Michaelia Cash moved in mid-August to end a period of post-election confusion when departmental bosses were trying to avoid talks, arguing they had been given no policy lead by their political bosses.

But in light of Senator Cash's order that there be no compromise on the terms of the bargaining policy, leaving departments with little or no room to manouevre in negotiations,The Canberra Times understands that some departmental secretaries and agency chief executives now see an opportunity to capitalise on weariness among their employees with the protracted stoush.

Public servants will also be told that the deals on the table are the best they can hope for after Labor, which had pledged to rip up the bargaining policy, failed to win government in July's federal election.

The Agriculture Department is understood to go to an unprecedented fourth attempt to convince its 4500 employees to sign up to a new deal by the end of September.

The department's third rejection of a deal offered under the bargaining policy came in March after an unusual intervention by its secretary Daryl Quinlivan, who told his workforce that a yes-vote would help in the fight against public servants who rorted their sick days.

A departmental spokeswoman told Fairfax on Friday that Agriculture would not be answering questions.

"The department doesn't have any comment to make about the progress of enterprise agreement negotiations today," she said.

John Lloyd, Australian Public Service Commissioner, on Wednesday said he was pleased to see that enterprise bargaining momentum was building, but was disappointed in the CPSU's campaigning activities against sensible offers.

"I believe the CPSU is doing its members a disservice by continuing to agitate for unrealistic pay outcomes in a constrained fiscal environment.

"Industrial action orchestrated by the CPSU has had a low participation rate and results in loss of income to those participating," he said.

The government's Workplace Bargaining Policy 2015 provides for affordable and competitive pay rises and the continuation of valued terms and conditions.

"Employees in agencies that have voted up their enterprise agreements are moving ahead in the knowledge that future pay rises are settled and a jointly supported enterprise agreement is in place. Many are about to receive their second pay rise," Mr Lloyd said.

The giant Defence Department wants to make it third time lucky by going to a vote of its 19,000 civilian workers before the end of October in a bid to reverse the result of two no-votes.

The Australian Communication and Media Authority has also indicated to unions that it wants a new vote to happen sooner rather than later.

In March, 76 per cent of ACMA's public servants rejected an offer that would have paid an average of 2 per cent a year, in line with the bargaining policy, for the three-year life of the agreement.

The Murray Darling Basin Authority is understood to want a vote soon, but is waiting until after the October school holidays to go to the ballots.