Federal Treasury staff have voted against the advice of their union to accept a pay rise that will likely be less than inflation.
However, the Community and Public Sector Union says the outcome does not reflect the mood elsewhere in the bureaucracy.
The Treasury is now the first department to approve a wage deal under the Abbott government, which has imposed tough rules on bargaining to restrain public servants' salaries.
About two-thirds of the department's eligible 823 staff took part in the ballot this week, and 58 per cent voted in favour of the proposed enterprise agreement.
Treasury officers will now receive pay rises totalling 4.5 per cent over three years: an immediate 2.5 per cent raise followed by 1 per cent increases in July 2016 and 2017.
However, their working week stretches from
The deal follows an agreement last month at the smaller Comsuper agency, whose staff accepted a one-off 2.6 per cent raise over three years.
However, most federal public servants remain locked in negotiations, even though their wage deals expired a year ago. Many have not yet had the chance to vote on an agreement.
The CPSU had told Treasury staff they deserve "a better deal than what is on the table now, particularly given the staffing cuts in 2014".
"It is important to vote 'no', because the Treasury offer is well below inflation, trades conditions for little gain, and strips rights into unenforceable policy," the union had warned before the ballot.
Employment Minister Eric Abetz welcomed on Friday what he said was a "significant" outcome.
"It is worth noting that Treasury is a financially literate and central budget agency," he said in a statement. "Treasury employees clearly understand the importance and the need for fiscal restraint as the government is faced with paying down the legacy of Labor's debt, waste and mismanagement."
It is believed only about one in 20 Treasury officers are CPSU members.
Staff at the tiny Australian Office of Financial Management, which is within the Treasury portfolio, also approved a similar deal this week.
Senator Abetz urged the CPSU to "stop standing between public servants and the responsible and affordable pay rises on offer in the current low-inflation environment".
He said inflation for the year to March 2015 was 1.3 per cent, while the Bureau of Statistics' latest data suggested employees' living costs were growing at just 0.2 per cent a year.
However, the government's own budget forecasts, published in May, say inflation is likely to be 2.5 per cent per annum over coming years.
Senator Abetz thanked "the overwhelming majority of public servants who continued to provide services to the public during the CPSU's recent industrial action".
The union's national secretary, Nadine Flood, responded that Senator Abetz was "
"Minister Abetz may think his current offers – including stripping rights and conditions worth significantly more than 1.5 per cent and even cuts to current take-home pay for thousands of workers – are responsible and realistic but I would suggest Immigration, Border Force, Centrelink and Medicare workers who have walked off the job in droves are sending rather a strong signal they don't agree," she said.
"We have seen before a few agencies vote agreements up, while the bulk of the public service holds out for better, fairer deals."