The 85-per-cent yes-vote, for a three-year deal with an average pay rise of 2 per cent per year, will be encouraging to other public service bosses around Canberra who are holding workplace votes this month.

The giant Defence Department will begin voting on Thursday for the fourth time on a proposed enterprise agreement and about 4000 Agriculture public servants are currently voting in an unprecedented fifth ballot.

Bosses at several departments have backed off the harsher elements of the Coalition's controversial public sector bargaining policy in an effort to finally settle the industrial disputes that have wracked government workplaces for three years.

With union no-vote activity at both agencies way down on previous efforts, hopes are high that workforces will finally accept the deals that have been offered.

Murray-Darling Basin Authority Chief Executive Phillip Glyde told his workers on Tuesday that the turn-out for the industrial ballot had been "fantastic".

"We had 264 staff vote, from the 292 staff who were eligible to vote," Mr Glyde wrote.

"This is a fantastic response rate of over 90 per cent.

"There were 224 staff that voted yes, and 40 staff that voted no.

"This is an 85 per cent yes vote.

"I am pleased to declare we have a yes vote!!"

Mr Glyde conceded that the bargaining process had been "long and difficult".

"It's been a long and difficult road and I'm pleased we now have an EA that the vast majority of our staff are comfortable with," he wrote.

The agreement must now be lodged with the Fair Work Commission, and it may be three weeks before the commission's process for approving the deal is complete.

Mr Glyde promised his workers, who have not had a general pay rise since 2013, that their wage increases would begin to be paid in the first pay cycle after FWC approval.