Public Servants at the Department of Industry have rejected a new wage deal in three-to-one workplace ballot drubbing.

The emphatic result, announced on Monday, came despite an unprecedented marketing blitz mounted by the department's bosses in the run-up to the poll.

With 76 per cent of the department's 3300 public servants casting votes, the wage proposal was rejected by 77 per cent to 23 per cent.

Unions campaigning for a no-vote were not confident before the poll, citing Industry's relatively low union membership and its record of an early yes-vote in 2011 when its public servants were last offered a deal.

The offer on the table, of about 1.6 per cent per year, was complicated by the task of achieving pay parity among a workforce that had been pulled together from various other departments during the upheaval in the public service following the 2013 election.

The result, believed to be the first time in decades that Industry Department officials have voted to reject a pay deal, leaves the government still searching for a departmental workforce to accept an offer under its tough public sector bargaining policy.

The no vote also came despite one of the most aggressive campaigns by a department seen in APS history, with Industry using well established union tactics against the CPSU in its push for a yes vote.

Officials at the department were hit with a "pop-up" on their computer screens when they logged on for work on Wednesday, an innovative last-minute touch to a slick, union-style marketing campaign mounted by Industry in a bid to have its proposal accepted.

Not even the toilets at the Industry Department provide a respite from the workplace battle.

Public servants have even been posted outside one of Industry's buildings in central Canberra, handing out flyers to their colleagues urging them accept the agreement.

"Pod talks" were convened around work stations in the department. Managers were  talking to small groups of staff and flyers urging a "yes" vote have appeared in kitchens, on noticeboards and even in bathrooms.

But acting departmental secretary John Ryan was brief and to-the-point in a bulletin sent out to all Industry staff on Monday, acknowledging the no vote.

"The executive considers that the proposed agreement was both responsible and fair and addressed the key priority consistently raised by staff, which was wage disparity," Mr Ryan wrote.

But the acting secretary conceded that he and his colleagues would now have to return to the drawing board

"However, as the proposed agreement has been voted down we will now carefully consider the result and seek employee feedback to determine what, if anything, contained in the proposed agreement can be modified to address employees' concerns.

"The executive remains committed to delivering all employees a fair and equitable agreement that the department can afford."

CPSU national secretary Nadine Flood claimed the vote as a significant win for her union, saying the tactics employed at Industry showed the government was desperate for a win.

"Despite the employer's best efforts to dress this deal up and pick what they described as a soft target with low union membership, their strategy failed spectacularly," Ms Flood said.

"The message from this result couldn't be clearer; the government's bargaining policy is completely broken and they need to sit down with the CPSU and discuss a more sensible way forward."