The giant Defence Department has been forced to concede it misled its workers on key aspects of its proposed new workplace agreement as its 20,000 civilian public servants begin to vote on the deal on Thursday morning.

Managers at Defence insisted, as part of a marketing blitz for their yes-vote campaign, that workplace protections stripped from the new agreement would remain enforceable.

But the after the department's main trade union cried foul to the Fair Work Commission, Defence has agreed to set the record straight.

Workplace rights and conditions are a key battleground in the disputes still raging after two years across the Australian Public Service.

Department's enforcing the Coalition government's hardline workplace bargaining policy have insisted from the start that rights are not being lost as enterprise agreements are "streamlined" with much of their content shifted to policy.

But unions have argued that policy is not enforceable by industrial authorities and can be changed by departmental bosses any time they choose.

Defence's marketing material re-iterated the position taken at other departments during their own disputes, with one bulletin assuring staffers that changes proposed to their agreement, the Defence Enterprise Collective Agreement (DECA), were there to make the document easier to understand.

"The proposed Agreement has been streamlined to make it easier for you to read," the bulletin read.

"Process and guidance are in policy.

"These policies are written directions from the Secretary to managers and staff and are enforceable."

As part of its latest marketing campaign aimed at reversing the close no-vote against the proposed new DECA in early March, posters appeared on the walls of Defence sites around the country stating plainly that  policy was enforceable.

"Anything in policy will continue to be enforceable and Defence will continue to consult with you," the posters read.

But under the terms of Defence's proposals, its employees would have no recourse to the Fair Work Commission for disputes arising from workplace "policies".

The Community and Public Sector Union asked the Defence hierarchy to issue a correction and when it refused, the union took its case to the Commission.

After two hearing at the Commission, Defence agreed to correct the record, issuing the following statement in the 67th of its bargaining bulletins.

"For the sake of clarity, there will not be an automatic right to access the Agreement's dispute resolution procedures regarding a dispute about a workplace policy," the bulletin read.

"The ability to bring a dispute about policy under the agreement relies upon the dispute being about a matter arising under the Agreement or in relation to the (National Employment Standards)."

The union told its members at Defence that the department had engaged in "appalling" and "misleading" conduct in its efforts to get its new workplace agreement over the line.

Another union went further, with Professionals Australia saying the department's top brass had "pants on fire".

"It's a begrudging but clear concession," union official Dave Smith told his members at Defence.

"Defence employees are being asked to give up a certain right to dispute resolution under the current agreement.

"The Department is probably hoping you don't realise their admission and the consequence for much of your conditions."

The Defence Department did not respond before deadline on Wednesday to requests for comment.