A decision by the industrial umpire has thrown the entire process into disarray after the Fair Work Commission found a failure to comply with a key technical requirement will render the whole bargaining process null and void.

Now workplace ballots are being cancelled or postponed and talks put on hold as departments and agencies realise they failed in their legal requirements at the start of the process and must now begin again.

The oversight, described by one union as a "massive stuff-up", throws into disarray efforts by departmental bosses to force the pace of the bargaining process after a period of post-election inaction.

The decision affects the entire Australian industrial relations landscape and came despite the intervention of employer lobbyists the Australian Industry Group, and the Australian Chamber of Commerce and Industry.

The majority decision by the full bench of FWC also means that large departments like Human Services and Defence may have wasted their time and taxpayers' money holding massive workplace ballots for agreements that never would have been legally approved.

The practical effect of the FWC decision, in a case against curtain manufacturer Uniline, is that even if a workforce votes yes to an the agreement, the deal cannot be legally ratified if the notices of employee representational rights had not been issued in accordance with the Fair Work Act.

The impact on the federal public sector bargaining is massive, Fairfax was able to establish that only three agencies, the Tax Office, the National Disability Support Scheme and IP Australia will be unaffected by the decision, although this list may grow in the coming days.

At CSIRO, a ballot scheduled for next week has been cancelled, posters are being torn down from workplaces and meetings and information sessions scratched from schedules as the science group goes back to the drawing board.

At the giant Department of Human Services, workers who have not had a payrise since 2013 after rejecting efforts to get them to agree to a new deal, have been told the bargaining process must begin again because of their department's failure to issue the notice of employee representational rights on time.

Human Services, a union stronghold where the dispute has been at its most bitter, has notified its workers that "the department has taken the decision to discontinue the current bargaining process so that a new process can commence as soon as possible."

The same technical oversight has put back the Department of Agriculture's fourth attempt to persuade its public servants to accept a deal and talks at the Murray-Darling Basin Authority have also been scratched.

Since the decision was handed down on August 25 many departments and agencies have discovered that their notices were issued late, throwing their enterprise agreement plans into disarray.

Dave Smith, a Canberra-based official with technical union Professionals Australia said the latest setback to the bargaining process mean that ordinary public servants would have to suffer "because of what's basically a massive management stuff-up."

The federal government's workplace authority, the Australian Public Service Commission, was contacted for comment for this article.