Vets working in the federal Agriculture Department are furious over a pay proposal that would reduce by $21,000 the annual wage of an entry-level vet in the department.

But the offer does not affect vets working in export abattoirs with public servants complaining the department is wary of the political heat that would result in industrial action at plants producing meat for the export market.

Insiders say the proposal is an "outrage" that has had a serious impact on the morale of the men and women whose task is to protect Australia from serious animal diseases.

But Agriculture says it developed the proposed new wage structure after consulting with its 320-strong veterinary workforce and that the new entry-level wage structure will improve the careers prospects of its up-and-coming vets.

The proposed new wage deal, which would have covered more than 4400 public servants at the Agriculture Department was rejected in a department-wide vote in December by a wafer-thin margin of just 62 votes.

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.

Agriculture frankly conceded to its workforce that the result had left the department's hierarchy in a quandary and searching for answers before it sat down again at the bargaining table this year.

But some of its vets say a good place to start would be the deal they were offered, which they say effectively splits the veterinary workforce between into two camps: those working in export abattoirs and everyone else.

Under the proposal, a mid-ranking veterinary officer level 4 would be starting on a salary $8000 lower than at present and would take four years longer to reach the top of pay band at their level.

Further down the pay scales, the top and bottom pay increments for level 3 vets would be stripped by $10,000 a year while Level 2 veterinary officers would have new pay increments of $17,000 less at the top and $13,000 at the bottom.

A new entry-level veterinary officer level 1 position was proposed, paying a wage worth $21,000 less than the current starting point of level 2.

But the pay scales of vets at export abattoirs would remain untouched under the proposal with departmental staffers complaining that the Agriculture is "not game to touch them" fearing the consequences of strike action on exports.

The department did not answer questions on why the two different pay scales had been proposed, but a spokesperson provided a statement saying the proposal was not about cutting costs.

"A number of changes to the veterinarian structure have been proposed as part of this bargaining round, reflecting previous feedback from the department's veterinarian officers," the spokesperson said.

"They are not cost-saving measures, but are in fact being explored to enhance the career progression and personal development of our employees.

"Negotiation on these aspects of the proposed Enterprise Agreement will continue when bargaining recommences for 2016."