Victorian Supreme Court Justice Claire Harris found it was in the public's interest for the two applicants to be named as they fight to stop the release of the Operation Richmond report.
But their lawyers immediately launched an appeal against the decision and the judge allowed a temporary pseudonym order to be in place while their fight goes to the Court of Appeal.
Operation Richmond, launched by the Independent Broad-based Anti-corruption Commission in 2019, investigated the Victorian government's negotiations with the United Firefighters Union.
They centred around reforms to merge Metropolitan Fire Brigade members and career Country Fire Authority firefighters into the new Fire Rescue Victoria.
IBAC commissioner Victoria Elliott indicated the final report would be released to the public by July 1 but that plan has been sidetracked by Friday's injunction application.
The two applicants are seeking to stop the report from being transmitted to parliament although grounds for their application were not aired in open court.
Their barrister Nick Wood SC also pushed for their names to be covered by a pseudonym, arguing any publication would render their application useless..
Mr Wood said the entire court file should also be closed, meaning media could not access any of the documents filed.
Media barrister Justin Quill opposed the applications, arguing the parts of the IBAC report that were being disputed could be suppressed but the applicants' identities should not be.
"It is hard to imagine a matter in this court that has a greater public interest," he told the court.
"This court is being asked to restrict the flow of information to our parliament. That is an extraordinary thing Your Honour is being asked to do."
IBAC also opposed the pseudonym order but the watchdog's submissions were heard in closed court without media present.
IBAC's barrister Frances Gordon KC did give an undertaking in open court, promising the corruption watchdog would not publish the report while the case was before the courts.
Justice Harris on Friday afternoon refused the pseudonym order application, finding there was insufficient reasons to grant one given the information already in the public domain.
But she granted temporary pseudonyms to the two applicants to allow their lawyers to challenge her ruling in the appeal court.
The judge also ordered the court file be closed, with the injunction hearing slated for late June also to be held in closed court.
There were reports Daniel Andrews, who was Victorian premier at the time of the firefighter reform negotiations, was questioned over Operation Richmond but he refused to confirm or deny that was the case.
Victorian Premier Jacinta Allan on Friday bristled at suggestions the delay in the report's publication was conveniently timed, with a state election six months away.
"The government is not a party to this matter and has no involvement in these proceedings," she told reporters.
The IBAC commissioner used the case to call for changes to legislation, arguing the current laws were limiting what the watchdog could share with the public.
"Victorians want - and should have - greater insight into what is being done to address allegations of corruption and misconduct," Ms Elliott said in a statement.
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