The proposed workplace agreement, which had been described as "harsh" by the main workplace union, was defeated by a 58 per cent no-vote in a result announced on Monday morning.

The ballot result comes as 17,000 public servants at the Defence Department, who have already knocked back three EBA proposals, prepare to vote again in mid-June.

Top Defence officials are hopeful that a front-loaded wages offer, which will see six per cent increases in the first 18 months of the agreement, will get their proposal over the line.

But public service union the CPSU says the lack of back pay, which is banned by the Coalition, might still be a sticking point for a workforce that has not had a general pay increase since 2013.

At the Bureau of Meteorology, chief executive Andrew Johnson told his workforce on Monday morning that just under 1400 BoM workers had voted and that the proposal had been rejected by 818 of them.

"The Bureau remains committed to putting in place an affordable EA that supports staff, which complies with the government's workplace bargaining policy," Dr Johnson wrote.

"We will return to the negotiating table and continue to bargain in good faith with our partners."

CPSU National Secretary said the BoM had stuck with the hardline industrial policies that had failed to secure agreement in most of the big departments, despite a general thawing of the atmosphere in recent months.

"Commonwealth bargaining will only be resolved when agencies recognise that protecting existing rights and conditions is a key concern for staff," Ms Flood said.

"BOM management moved on some very minor sticking points but largely ignored the more constructive approach being taken elsewhere and instead continued with a harsh and divisive agreement that particularly targeted unfair cuts at frontline staff working shifts and in remote locations.

"We're not at all surprised that BOM workers have given this dud deal the thumbs down."

"In contrast, we've worked very hard with a range of other agencies over recent months, making progress as they've realised the need to take cuts to rights and conditions off the table.

"That in depth work is why in some workplaces we are in a position for CPSU members to decide not to oppose enterprise agreement ballots."

At Defence, the union is adapting a more conciliatory tone, telling public servants at the giant department that the offer on the table is much improved while stopping short of actively endorsing a Yes-vote.

The CPSU also told members that it believed a better pay offer was unlikely.

"While we cannot endorse the Defence EA proposal as it does not deal with key issues such as back-pay and the movement of conditions into policy, we recognise that some key conditions have been protected and are enforceable," the union wrote.

The ballot will be held between June 15 and June 20.