The massive Defence Department has voted to reject a new workplace agreement proposal developed under the Coalition's hardline industrial relations policy.

The department's 18,000 public servants rejected the proposed deal by a margin of nearly 55 per cent to 45, an increase on last month's knife edge no-vote.

Departmental boss Dennis Richardson, who campaigned hard for his workers to accept the proposed agreement, acknowledged the result in a message to staff on Wednesday morning.

"84 per cent of staff voted on the proposed enterprise agreement. Of those, 54.86 per cent voted 'no' and 45.14 per cent voted 'yes'," Mr Richardson wrote.

"I thank everyone for their active participation.

"We will advise next steps over the coming weeks."

Attention will now turn to another massive workplace ballot underway at the Australian Taxation Office, likely to be the last chance for the government to persuade a large group of public servants to accept an enterprise agreement under its controversial public sector bargaining policy before an election is called.

In the wake of the Defence vote, technical union Professionals Australia was out of the blocks early, criticising the conduct of the Defence hierarchy in the lead-up to the ballot.

"This is a hammer blow to a deceitful, mean approach to workplace relations," union official Dave Smith said.

"Employees saw the timing of this vote as a cynical attempt to rush through the ballot before the election and were appalled by the attempts of senior Defence leadership to mislead them on critical changes to the proposed agreement."​

Last week the department was forced to concede it misled its workers on key aspects of the proposed agreement after a union complained to the Fair Work Commission.

Mr Smith said staff at the department had told him the admission was a factor in the no vote along with the looming double dissolution election.

CPSU National Secretary Nadine Flood said the result was embarrassing for defence management and the government.

"They threw massive resources into this ballot yet support for the unfair and unreasonable offer they put on the table went backwards," she said. "Defence staff have shown they are holding out for a fair deal."

"This no vote shows defence staff didn't take kindly to misleading statements from the department, falsely claiming that rights and conditions stripped out of agreements and moved into policy remained enforceable."

Late last month, the federal opposition announced it would dump the Abbott-era bargaining policy that led to nearly two years of industrial action, in a bid to win marginal votes.

Labor's defence spokeswoman Gai Brodtmann described the vote as a "significant stance" against the government's bargaining policy.

"The percentage of people voting down the agreement has actually increased from the last defeated ballot," she said.