Department of Defence secretary Dennis Richardson believes a revised pay deal – to be put to vote on February 25 – will inevitably disappoint many public servants.
Negotiations between the department and unions ended in early February although the Community and Public Sector Union has already condemned the offer.
The existing agreement nominally expired more than 18 months ago and the new one was unlikely to take effect until mid-2016.
Mr Richardson said the new offer, which includes a six per cent pay increase over three years, would be comparable to offers accepted by other departments.
"I think it would be fair to say that some people would remain unhappy and that would not surprise anyone," he said. "Equally I think we have put on the table the best possible offer we can."
"What we have put on the table is the same, or better, than other agreements that have been approved by staff in some other departments."
Defence Minister Marise Payne said she was satisfied with the department's handling of the negotiation process and was regularly briefed.
"Agreement is a two way street and I think the department and senior officers are working with the unions and reps and staff to engage in appropriate discussion around this process," she said.
Mr Richardson said there was not ability to revise the offer if rejected by staff, while working within government restraints.
"Quite obviously we are required under legislation to go back to the bargaining table," he said. "The wage outcome is, as it always has been, determined by policy and that policy is clear and has been articulated publicly."
CPSU national secretary Nadine Flood said the new offer would hurt Defence's civilian staff.
"The hard working civilians working in Defence face losing significant rights and conditions while still leaving them well behind the ADF in terms of wages, given the ongoing department pay freeze," she said.
"Defence has tinkered round the edges of the last draft but the real problem is it's still negotiating on the basis of a fundamentally unfair government bargaining policy that requires agencies to summarily strip rights and conditions."
Dennis Richardson said SES workers within the department had not received a pay rise since 2013, although he confirmed his own income had increased by $85,000, taking his base salary to $814,000.
The pay increases for Mr Richardson and other secretaries were approved before Christmas despite many departments continuing to negotiations and many rank-and-file public servants going without a pay rise since mid-2013.
Professionals Australia director Dave Smith said Mr Richardson was not getting 40 times the salary increase compared to a base level EL1 staffer and 60 times the increase compared to an APS4.
"The Department head and the ADF have had their pay and conditions determined by an independent tribunal," he said. "Maybe it's time for the civilian workforce to have their salaries determined the same way."
In December, Mr Richardson announced to staff the department could raise its offer to 6 per cent over the three years with much of the pay increase front-loaded early in the life of the agreement.
Defence is one of the biggest organisations, according budget and staff numbers, to be at the negotiating table during talks across the bureaucracy affecting the pay and conditions of 150,000 public servants.