Staff at Fair Work Building and Construction have voted by a margin of 63 to 37 per cent to reject the latest enterprise agreement proposal.

Meanwhile, workers at another government workplace the Civil Aviation Safety Authority, have voted to accept a deal.

Workers at the construction watchdog were told on Tuesday that 82 per cent of the 140 public servants there had voted on the latest proposal from management with 72 public servants voting to reject the deal and 43 staff voting to accept.

Remarkably, 26 staff members, or nearly 20 per cent of the workforce have appointed themselves as bargaining agents in the EA process.

The agency's human resources boss Josh Banks conceded it might be some time before another proposal is put before its workforce.

'We will now need to take some time to consider our next steps, which will include understanding the reasons behind the outcome of the ballot," Mr  Banks wrote to his colleagues.

The public service's main workplace union, the CPSU, says the vote, by an agency best known for its frequent legal stoushes with construction union the CFMEU, "speaks volumes" about how public servants view the government bargaining policy.

"The fact that even in a place that is not a union stronghold, this has been voted down, just demonstrates how toxic the Turnbull's bargaining policy really is," CPSU deputy secretary Beth Vincent-Pietsch said.

"Even in FWBC, it's been rejected.

"So this offer is interesting, this isn't one where they can say there are large numbers of union members there, this is a union-busting agency still rejecting an offer made under the bargaining policy, so this one is really important."

The union official said she and her colleagues had observed government employers taking a hard line in negotiations after talks had resumed following a period of relative quiet before and after the federal election.

"The government just had very small movements in their offers and  no matter how divisive it was in the workplace, they were just going to barge it through," Ms Vincent-Pietsch said.

"That is tough for our members, because it's been three years without a pay rise, three years of campaigning."

Meantime, workers at the aviation authority voted by a 55 to 45 per cent margin to approve an agreement offered under the government's controversial policy.

Announcing the ballot outcome on Friday, the authority's chief executive Mark Skidmore acknowledged that hundreds of CASA employees had voted against the deal.

"An encouraging 86 per cent of eligible staff voted meaning that the majority of CASA staff have had the opportunity to have their say," Mr Skidmore wrote to his colleagues.

"The results tell me that while the yes vote prevailed, there were many of you who did not support the offer.

"I assure you that the consultation mechanisms will be put in place to provide you an avenue to continue to have your say."