Workers at the Department of Agriculture voted by a margin of 67 per cent to 33 per cent to reject the pay offer of 1.5 per cent accompanied by cuts to various entitlements and conditions.

The vote comes on the heels of an emphatic rejection of a similar deal on Monday by a large majority of public servants at the influential Department of the Prime Minister and Cabinet.

In a relatively low turnout at Agriculture, fewer than 3500 of nearly 4600 eligible employees cast their ballots in the vote with the result announced on Tuesday.

The vote is a fresh blow to hopes that deals can be agreed between most government agencies and their workforces under the tough bargaining position after large departments like Human Services, Health and Immigration have all voted to reject offers of 1.5 per cent.

Agriculture workers, unhappy at the progress of wage talks, had already resorted to industrial action, with repeated short strikes and work bans by quarantine and biosecurity staff, including at export meat plants, airports, ports and mail centres even before the offer was put to the vote.

Notifying his colleagues of the result, senior department executive Tim Chapman indicated that industrial peace at the department, which also administers the nation's water resources, was some way off.

"As a consequence of the no vote we will return to the bargaining table, though it is too early at this stage to say when this could occur," Mr Chapman wrote in his all-staff bulletin.

"Please let me know what your thoughts are in this regard."

The main workplace union, the CPSU, said the Agriculture vote was another sign the government's bargaining policy was in deep trouble.

The union's national secretary, Nadine Flood, said the deal offered to Agriculture workers was "unfair".

"Yesterday it was a 78 per cent no-vote from staff in the Prime Minister Malcolm Turnbull's own department, Prime Minister and Cabinet," Ms Flood said.

"Today, two out of three Agriculture Department workers have clearly rejected an unfair deal that would have cut their rights and conditions in return for an 18-month wage freeze and then just a 1.5 per cent a year pay offer."

Ms Flood made it clear that her union did not intend to allow Public Service Minister Michaelia Cash to forget about comments made last week about public servants not living "in the real world".

"New Employment Minister Michaelia Cash declared last week that public sector workers need to live 'in the real world' and there is no public sector bargaining 'mess', yet there have already been two agencies vote no to deals just this week, showing just how messy and unrealistic the government's current bargaining policy is," Ms Flood said.

"Minister Cash says she wants to apply real-world standards of productivity to the public service, but no Australian company would expect its staff to pick up the massive extra workload created by 17,700 job cuts, go through major restructuring and then tell its workers that doesn't count and they've delivered no productivities."