But unions are campaigning hard for a no-vote, saying the proposal on the table erodes workplace rights and offer pay rises of just 1 per cent per year, when the years of delays are taken into account.

Public servants in the giant Defence Department were told on Tuesday night that they had rejected for the third time an enterprise agreement offered under the hardline public sector bargaining policy, with an increased No-vote of 58.4 per cent.

Departmental boss Dennis Richardson thanked his staff for their votes and saying the issue would be revisited in 2017.

At the Tax Office, human resources boss Fiona Dillon took to the video channel in an effort to get a yes-vote over the line at third time of asking, telling ATO workers that their conditions and entitlements were safe under the proposed agreement but that there would be no back pay.

"With very few exceptions, the entitlements you have under the current 2011 agreement have been maintained in the proposed EA or otherwise covered by legislation," Ms Dillon said.

"As an organisation, we will also continue to seek to enhance the staff experience, as we have done in the past, by making improvements and supporting you in ways that go well beyond what is mandated by the EA.

"With regards to our remuneration proposal the bargaining policy allows a maximum pay increase of 6 per cent reasonably spread over three years, with no option for back pay.

"Our offer gives you this maximum 6 per cent pay rise with 3 per cent on commencement, 2 per cent 12 months later and a final 1 per cent another 12 months after that."

Ms Dillon said ATO public servants should not get their hopes up over the Immigration Department being forced into arbitration with its workforce, or the savaging of the government's policy by a Senate committee.

"The government is not bound by any recommendations of the senate inquiry and the circumstances that lead Department of Immigration and Border Protection to arbitration do not apply to us," she said.

"In light of this, if we receive a no vote I expect we will recommence bargaining under the same workplace bargaining policy."

But the main workplace union, the CPSU, backed by the smaller Australian Services Union, says voting for the agreement will take employment conditions at the ATO backward.

ASU official Jeff Lapidos told his members in a bulletin that a no-vote would increase the pressure on Commissioner of Taxation Chris Jordan to find a settlement to the dispute.

"We ask that you make a short term sacrifice by voting no again so together we can achieve a new ATO Enterprise Agreement that provides maximum support for your job security and your job satisfaction," Mr Lapidos wrote.

"We are confident that Commissioner Jordan will agree to meet our needs because he needs to get a new Enterprise Agreement in place. The process has dragged on far too long for him as well as for us.

"We haven't been able to get the Commissioner to improve his proposal enough because he formed the view that he has improved his proposal enough to get a new Enterprise Agreement across the line."

Voting closes at 2pm, Wednesday.