The Department of Immigration and Border Protection's revised enterprise agreement will result in 680 redundancies, senior bureaucrats say, three times more than initially expected.
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Department secretary Michael Pezzullo said additional job losses were "an unavoidable reality" after 91 per cent of employees rejected a pay increase of 3.4 per cent over three years, one of the lowest offers in the public service.
The initial pay offer, which was rejected late last year amid stopwork meetings at international airports across the nation, would have resulted in 184 full-time equivalent redundancies.
Mr Pezzullo said the initial offer was drafted to "keep employee reductions to an absolute minimum over the life of the agreement to ensure we had sufficient resources to carry out our duties as set by government".
"I am keen, as is the [Australian Border Force commissioner Roman Quaedvlieg], to ensure that these reductions are kept to an absolute minimum."
Deputy secretary Dr Jill Charker, who leads the department's negotiation team, said bargaining resumed with union representatives last week.
"There are issues that have popped up during this period and also things we put on the table for consideration that we are still working through," she said. "Clearly, our intention is to work expeditiously in this space to give our staff an opportunity to vote on the second offer."
Mr Pezzullo said the department was working to create as generous an offer as possible for staff while working within the government's parameter.
"We are keen to develop an enterprise agreement that delivers the greatest benefits to the largest number of employees and one which also recognises the challenging nature of our reform and integration environment, our increasing operational demands, and, of course, our budgetary constraints," he said.
Late last year, Mr Pezzullo admitted parts of his workforce were lacking motivation, morale and job satisfaction after a drawn-out negotiation period.
Union members in the department walked off the job for 24 hours in November as part of their wage dispute.
Stopwork action caused delays at eight international airports in September.
The Immigration Department and the Customs Service merged in late 2014.
Mr Pezzullo described the integration programs as "large and complex".
"They affect around 14,000 staff across the portfolio as well as our financial, legal, infrastructure, technology, and organisational policies and processes," he said.
"We are committed to building one culture and one organisation; an objective which includes continuing to consolidate and streamline functions across the portfolio."
Mr Pezzullo said consolidation within the department would save the government $270 million over the forward estimates.
"By the end of this financial year, it is our expectation the bulk of [the] integration effort would have been completed, with the expectation of some core elements like full IT integration and property consolidation."
Last year, a tender to build a department headquarters, which would have meant 4000 workers left Belconnen, was withdrawn days after the Department of Finance updated its property lease protocol.
Mr Quaedvlieg said the Australian Border Force workforce had grown to 6000 with an additional 225 officers beginning operational work at airports since June.
