Civilian workers in the Defence Department are furious at their exclusion from wage concessions granted to their uniformed colleagues by the Abbott government on Wednesday.

Unions representing Australian Public Service staffers in the sprawling Defence establishment say a yawning pay gap will now open between uniformed personnel and their civilian colleagues.

But the Prime Minister and the public service minister say the public servants have done much better for pay rises than the sailors, soldiers and Air Force personnel over the past decade.

The ADF will now be offered 2 per cent per year, an increase on the 1.5 per cent offer that sparked outrage and a grass-roots protest campaign by military families in late 2014.

The move follows an earlier backdown which saw the government abandon plans to cut military conditions and entitlements as part of the three-year deal.

But the Defence Department confirmed on Wednesday that there would be no such good news for Defence's 20,000 public servants who have been offered just 1.05 per cent per year which comes with deep cuts to leave, entitlements and conditions.

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The Prime Minister's cave-in on military pay on Tuesday moves further away from the long-established principle that wages in the ADF and the Defence Department should move in unison.

Unions, who were already seeking permission to begin a campaign of industrial action in the department, were unhappy on Wednesday with the technical union Professionals Australia saying its members deserved to have their pay keep up with their uniformed colleagues.

"Our members are effectively the fourth arm of defence, they are the force behind the forces," union official Dave Smith said.

"They were outraged when the government imposed the 1.5 per cent position on (ADF)  personnel last year.

"When that pay deal occurred the government said it was the best they could do – it obviously wasn't."

The Community and Public Sector Union said that public servants, who also served their country, deserved a fair pay rise, too.

"Offering our ADF 2 per cent with no cuts to conditions isn't exactly generous, but it is a mile ahead of the attack on rights and real wages on offer from this government to public sector workers," CPSU National Secretary Nadine Flood said.

"If the government can move for our ADF personnel, why don't Defence civilians and the public sector workers who protect our borders in Customs, Immigration and Quarantine deserve more than a vicious attack on their rights and conditions?"

In Senate Question Time on Wednesday, Senator Abetz produced figures which he claimed to show that public servants had enjoyed a better pay rise deal than sailors, soldiers and Air Force personnel.

"Over the decade from 2004 to 2013, annual ADF pay increases have totalled 38 per cent while annual median wage increases for Commonwealth public servants totalled 42 per cent compared to CPI totalling 28 per cent," the minister told the Chamber.

"In other words, public servants have done about 4 per cent better than members of the ADF.

"ADF personnel fell behind members of the Commonwealth public service under the previous Labor government.

"In the years 2008-2013, annual ADF remuneration increases totalled 21 per cent while APS increases totalled 26 per cent."