Internal documents from the Department of the Prime Minister and Cabinet reveal "significant concern" among staff over the fate of their 15.4 per cent guaranteed annual superannuation contributions.

The documents were compiled this month and indicate the government still has much to do in its efforts, led by public service minister Eric Abetz, to convince its 160,000 public servants that their super is safe, despite winning the backing of the Fair Work Commission for its position.

PM&C, like many other Commonwealth departments, is battling to convince its 2400 public servants to accept the new three-year enterprise bargaining deal on offer.

The Community and Public Service Union has stoked concerns among staff over their generous 15.4 superannuation guarantee, which the government wants to strip out of departmental agreements, arguing it is protected by legislation and that its presence in the agreements is simply duplication and unnecessary red tape.

The union insists the move would leave the government free to try to reduce the payment to the 9.5 per cent paid to most workers, and the CPSU's campaign looks to have gained some traction among the retirement-conscious Commonwealth workforce.

But the Fair Work Commission backed the government in January, 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 PM&C staff are yet to be convinced: internally circulated documents note that super remains a big worry for the workforce in the current bargaining round.

The document said: "Significant concern over the removal of the reference to 15.4 per cent contribution rate from the draft agreement."

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Elsewhere, the papers note worries about the loss of allowances and entitlements, particularly among the hundreds of Indigenous affairs bureaucrats drafted into the department in 2013 and 2014, who were already more poorly paid than their new colleagues.

There was also a repeat of the concern, seen across the service that the pay rise offered, just 0.7 per cent per year, was more than cancelled-out by the extra working hours being demanded and "the concern that the pay offer does not adequately compensate for loss of conditions".

The Canberra Times reported last week that the department's bosses were reluctant to put their proposal to the vote, anxious about a repeat of the politically embarrassing scenes at Senator Abetz's Employment Department, where its 1800 public servants voted in a landslide to reject the deal they were offered.

PM&C bosses have indicated they are willing to compromise on aspects of the deal on offer but have also said the government's tough bargaining framework rules leave them little room to manoeuvre.

Senator Abetz's office did not respond to requests for comment.