The latest rejection, by just 10 votes, came after the authority's boss brushed aside the result of the last ballot in October and pushed ahead with a fresh vote on the same agreement, claiming he wanted all eligible staff to have their say.

It is the third time MDBA employees have rejected an enterprise agreement.

But the latest ballot attracted an increased 91 per cent turnout and a higher no-vote and the agency's Chief Executive Phillip Glyde says he now has "great confidence" that the ballot result reflects the wishes of his staff.

"We had an excellent turnout with more than 90 per cent of all eligible voters casting a vote," Mr Glyde wrote.

"This is a significant improvement on the last ballot and it gives me great confidence that the outcome of the ballot reflects the wishes of all staff.

"As a consequence we will now return to the bargaining table and re-commence negotiations. We will provide the details of who, how and when in due course."

Community and Public Sector Union Deputy Secretary Beth Vincent-Pietsch said putting an unchanged offer out to a second vote "disrespected" the authority's 300 public servants.

"Well the proof is in the pudding, a fresh rejection, the third 'no' vote at MDBA and this time with increased participation to 90 of staff," Ms Vincent-Pietsch said.

"Now MDBA workers will get to keep their hard-won and valued rights and conditions and management have committed to get back to the bargaining table for some further negotiation

"This 'no' vote was a tight result in a smaller agency but it's absolutely symptomatic of the problem across Commonwealth bargaining."