The result was a case of third-time lucky after the workforce in Public Service Minister Michaelia Cash's own department twice rejected deals, most recently in December by a similarly close margin.

Of the 1655 votes cast, 876 public servants voted yes to the deal that pays average wage increases of 2 per cent a year and 779 voted no, a winning yes-vote margin of 49 votes, or 3 per cent.

Elsewhere in the 150,000-strong Australian Public Service, mixed results are coming back from the present round of workplace ballots as departments and agencies try to extricate themselves from pay disputes that have been rumbling on since 2013 in some cases.

A wage offer was smashed, for the second time, at the giant department of Human Services last week by a margin of nearly 80 per cent to 20 per cent while the Australian Electoral Commission returned a 60 per cent no-vote.

In Defence, another behemoth department, an offer of 6 per cent over three years will go to ballot of its 19,000 public servants next Thursday, with the result keenly watched across the service.

The Community and Public Sector Union has been scathing of the inability of former Employment Minister Eric Abetz and his successor Senator Cash to persuade public servants in their own department to accept the deals on offer.

The union's national secretary Nadine Flood described the result on Thursday as "disappointing" but a "line-ball" outcome.

"Line-ball votes like this one signal a divided workforce, a million miles from Malcolm Turnbull's vision of innovative, productive and engaged workers," the union leader said.

"This is a disappointing result because we believe Department of Employment staff deserved a better deal and the fact remains that there are deep-seated concerns about these agreements, including from some of the staff who have voted for them."

But Ms Flood said the majority of public servants were still rejecting the deals offered under the Coalition's tough public sector bargaining policy.

"All up around 85 per cent of APS workers still don't have a new agreement and across the service the vast majority of people continue to emphatically reject dud deals based on the government's unfair public sector bargaining policy," Ms Flood said.

"It's less than a week since nearly 80 per cent of workers voted No in the largest Commonwealth agency, the Department of Human Services.

"Staff have recently voted in their thousands at other major agencies, with an 85 per cent No vote at the Australian Taxation Office and 91 per cent No vote at the Department of Immigration and Border Protection.

"This outcome won't change the fact that most of the ordinary mums and dads working in APS will keep on fighting until they get new agreements that protect their rights and conditions, and there's a reasonable pay offer on the table."

The minister welcomed the result on Thursday.

"Bargaining is a matter for agencies," Senator Cash said.

"I welcome this week's successful ballot – this is positive news for employees who will now receive a pay rise."