NCA staff narrowly voted up a new industrial agreement in mid-May expecting to receive their first pay rise soon after, but learnt a mishap with documents in the bargaining round would keep them waiting.

Authority bosses had expected changes to federal industrial relations laws would resolve the problem, but decided to restart enterprise bargaining from scratch after it became clear the legislation would not be passed until at least November.

Despite calls from the main public sector union for staff compensation, the Australian Public Service Commission has stopped the NCA backdating any pay rise to May, deciding it was banned under the Coalition's workplace relations policy.

Community and Public Sector Union deputy secretary Beth Vincent-Pietsch said the refusal of compensation for delays beyond staff control was "mean spirited and completely unfair."

"A Commonwealth-wide ban on backdating pay rises to previous agreements was already unfair but this situation is even worse," she said.

"This stuff-up is going to cost the average capital authority staff member thousands of dollars, as they head into their fourth Christmas without a pay rise.

"The fact this can happen again highlights that the current rules around enterprise bargaining are broken and need to be fixed."

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Acting NCA boss Andrew Smith said it was committed to engaging with staff and resolving the discussions about the authority's enterprise agreement.

"The NCA will also continue to meet the standards expected of all Australian government agencies as set out in the Australian Public Service Bargaining Framework", he said.

The public service commission said wage increases had to be prospective under the government's workplace policy.

"This means that pay rises are to apply from the commencement date of a new agreement, after approval by the Fair Work Commission," a spokeswoman said.

"This has been a longstanding policy principle across successive governments."

In May, 54 per cent of staff at the planning authority voted to accept the proposed pay deal, with 80 per cent taking part in the vote, before learning a document was mistakenly issued on an official letterhead and wrongly included information in breach of workplace relations rules.

In an email to the authority's 50 staff in October, Mr Smith said there was no clear path for a resolution to the problem and he was opting to return to stage one of negotiations.

The key element of the blocked legislation would allow the Fair Work Commission to overlook minor procedural or technical errors when approving enterprise agreements, provided the errors would not have disadvantaged employees.

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