The case has been running for several years and has already cost taxpayers millions in legal fees and other Commonwealth resources. While the Court of Appeal Justices Chris Maxwell, Marcia Neave and Paul Coghlan might have saved the case from an embarrassing collapse, they too found the AFP and ACIC to have acted unlawfully during their investigation. At the heart of the controversy was the ACIC's decision to use its exceptional powers – which allow it to compel a suspect to answer questions or face imprisonment – to unfairly and unlawfully aid the AFP investigation. The ACIC exists to provide law enforcement with intelligence on and analysis of criminal activity. It is not meant to use its powers to directly question suspects who have or are likely to be charged with criminal offences on behalf of police.

But this is what the ACIC did by allowing several AFP officers to sit in on the examination of suspects and by producing a transcript of the questioning for the benefit of other federal police officers and Commonwealth prosecutors. "[The ACIC examiner] was well aware that the examinations were intended to further the investigation and prosecution … he knew that, as part of that, the AFP wanted to have them locked in to their account on oath, for use against them in relation to a future prosecution," the Victorian trial judge found. The Court of Appeal justices agreed with the trial judge's finding of unlawful conduct. But they differed on the question over whether it was reckless, taking into account submissions from the AFP and ACIC stating that their officers had misunderstood a vital part of the Act which gives the criminal intelligence agency much of its powers. Most importantly for those running the prosecution, the Court of Appeal justices found there was no basis for ordering a permanent stay on proceedings because neither the trial judge nor the lawyers for the accused were able to identify how the unlawful examination process had actually damaged the prospect of a fair trial.

This was despite the lawyers for the accused men spending 30 days cross-examining officers from the AFP and ACIC about their dealings and motivations. Several AFP investigators testified that they had already gathered most of their evidence against the executives and prepared prosecution briefs prior to the ACIC examinations. Despite the failure to identify any instances of harm caused to the suspects' rights to a fair trial, the trial judge ruled that it was "highly probable" the AFP investigators got an unfair advantage by using their knowledge of what was said in the secret hearings to aid their searches for incriminating documents. The Court of Appeal concluded the trial judge had no right to make such a finding. "The issue of forensic advantage not having been explored and the AFP officers' denials not having been challenged, her Honour was not in a position to doubt the veracity of the AFP officers' evidence or to draw the inference which she did."

The Court of Appeal judgement reveals that the Commonwealth will install a new prosecution team to remove any doubts about having improper knowledge as a result of getting access to the ACIC examinations. As a final word, the Court of Appeal justices said it was the job of trial judges to find a way to overcome obstacles to a fair trial rather than "refusing to exercise the jurisdiction to hear and determine the issues". "By the flexible use of the power to control procedure and by the giving of forthright directions to a jury, a judge can eliminate or virtually eliminate unfairness. "The judges's responsibilities are heavy but they are not discharged by abdication of the court's duty to try the case." Fairfax Media understands lawyers for the accused men are considering seeking leave from the High Court of Australia to appeal the decision to overturn the permanent stay order.