The full draft agreement, unveiled by the Department of Immigration and Border Protection to its 13,500 public servants late last week, looks set to spark an escalation of the newly formed department's industrial woes.

The department says the deal "delivers an affordable outcome with a range of enhancements across the integrated workforce".

But one workplace source said: "It's gone down like a bucket of cold sick" and the department's main union telling its members that the offer "doesn't stand a chance of being accepted".

The pay offer, of just over 1.1 per year, is well below the 1.5 per cent offers that are being rolled out across the Australian Public Service.

But it is the confirmation of deep cuts to allowances and conditions, that have long been an important component of take-home pay packets in the pre-merger Customs agency, that are expected to be the main flashpoint between the border guards and their bosses.

Customs officer were paid a range of allowances for duties including being at sea for weeks at a time, using firearms, meeting high fitness standards, working long hours, unusual shifts and dirty or dangerous work

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Allowances for officials transferring to the Border Force were rolled over in an attempt to facilitate a trouble-free launch of the politically charged new agency in July.

But although the draft agreement confirms that the payments are slated for the chop, a departmental spokesman said Border Force members would get a composite allowance and that the proposed deal allowed for higher salaries than the current EA.

"The proposed agreement offers a range of beneficial outcomes for the integrated Department; including new top of range salaries that are higher than those currently available under the Department's current EA, and a new Border Force Composite Allowance," he said.

"While individual outcomes will vary, the combination of general increases and higher ranges equates to an average pay increase of 4.5 per cent over the life of the agreement."

The spokesman added that the proposed deal allowed the department to keep job losses to a minimum during its three-year life.

But the union is not happy with the proposal.

"Cuts to a range of allowance which will leave many employees in Border Force and the Department up to $8000 short with some employees is remote areas up to $20,000 behind," according to a CPSU bulletin sent out to employees.

"Hours of work will increase for former ACBPS employees by 2.04 per cent, nine minutes a day, every day every week every month.

"That is an extra week worked every year."

The agreement must be accepted in a ballot of the department's workforce if it is to be accepted but according to the union's call to arms, a yes-vote is unlikely.

"The CPSU bargaining team has repeatedly told the Department that this offer doesn't stand a chance of being accepted and that remains the case," the bulletin states.

The union's national secretary Nadine Flood said the offer was "mean and tricky".

"This disgraceful offer fails to recognise the hard work and professionalism of Border Protection workers. For them it's a kick in the guts," she said.