Public servants at the Murray Darling Basin Authority were asked to vote on a six per cent pay increase after the federal government relaxed pay restrictions in October.

On Wednesday, an internal ballot found 58.9 per cent of staff rejected the offer with a participation rate of 87.3 per cent.

"This is an excellent figure and demonstrates the high level of engagement by staff," an internal email from MDBA executive director Russel James said.

"The result of the ballot is a true reflection of the views of the majority of staff and as such I am confident that our consultation process has been inclusive and informative."

Under the proposed agreement, staff would receive a 2.5 per cent pay rise at the start of the first year followed by 1.75 per cent at the beginning of the second and third years.

The Community and Public Sector Union has said rights, conditions and take-home pay were the most important issues for members after analysing the results of a 7000-member survey recently.

Staff were given five work days to anonymously vote on the new proposal from last Thursday.Before the vote, Professionals Australia ACT spokesman David Smith said the pay increase was an improvement but "you would have to be a mug to vote up an agreement when the offers are likely to improve". Mr James thanked staff for being "actively involved" in the negotiation process.

"As a result of the outcome of the vote the executive will consider next steps," he said. "I will advise staff once we have had that discussion."