The department's bosses were expected to have got their proposal over the line with an improved wage offer and by cutting a separate deal with the department's most militant group of workers, the meat inspectors.

But Agriculture's staff were told on Thursday morning that the proposal had fallen agonisingly short, with 80 per cent of the department's public servants casting ballots, in a result that will send both sides back to the negotiating table in the new year.

The result follows another close-run vote this week at the Employment Department where workers voted by a 55 per cent to 45 per cent margin to reject the deal on offer.

Agriculture's lead negotiator frankly conceded in an email sent out to thousands of workers on Thursday that the result left the department searching for answers.

"The outcome leaves us in a quandary," the senior executive wrote.

"As you know, at each stage we have made the best possible offer and unless there is another change in the government's bargaining policy, the department's current pay offer will not be able to be improved in 2016.

"As you would also know, beyond the current offer, there are more difficult questions about affordability and the impact on staffing levels."

Technical union Professionals Australia, which represents veterinary and agricultural scientists working at the department, said the rejection meant that workers there were still worried about cuts to conditions and entitlements.

"Scientists and engineers sent a message to Barnaby Joyce in the Murray Darling Basin Authority and they are sending him a further message here from the Agriculture Department," union official Dave Smith said.

"It's not just about general pay increases, which aren't good enough, it's about valuing and recognising veterinary and agricultural science expertise.

"If this government is serious about an innovation agenda they need to ensure that they value their own expertise as a starting point."