The ACT Court of Appeal has found the judge, Acting Justice Anthony Whealy, may be seen to be biased when contemplating "very serious" allegations about misconduct and ethical transgressions by the prosecution at Eastman's original trial in 1995.

That's because Acting Justice Whealy's old judicial colleague, Michael Adams, led the prosecution of Eastman, which has since copped criticism for failing to give the defence material that could have helped discredit forensic evidence linking him to the crime scene.

"[Acting Justice Whealy] will most likely be required to assess whether evidence given by Mr Adams, including evidence given before him, is honest and reliable," the ACT Court of Appeal said on Wednesday.

"The history of the matter is extraordinary and the stakes for all concerned are high.

"Mr Eastman spent over 19 years in prison following what is now accepted as having been a deeply flawed trial involving, at best, serious errors of judgment by the Crown and, at worst, serious prosecutorial misconduct."

The decision means it is now unclear who will hear Eastman's stay application, a problem complicated by the fact that so many of the territory's judicial officers already have past involvement in the long-running legal saga.

It also raises the prospect of further delays to the case, forcing the court to find a new judge before Eastman's stay application is heard next month.

Acting Justice Whealy was brought in by the ACT Government to hear Eastman's retrial for the 1989 murder of Assistant Federal Police Commissioner Colin Stanley Winchester, and to preside over his stay application.

Wednesday's decision will prevent Acting Justice Whealy from hearing the stay application, but does not affect his involvement in any retrial of Eastman.

Eastman had tried to remove the judge on the basis that he may be seen to be biased by reasonable and fair-minded bystanders.

That apprehension of bias, it was argued, could arise due to the 12 years he spent working with Mr Adams on the NSW Supreme Court bench.

Eastman argued that hearing the stay application may force Acting Justice Whealy to make judgments on his former colleague's propriety and conduct during his time prosecuting the Winchester murder case.

The prosecution failed to disclose "highly relevant" material to the defence casting doubt on the now-discredited evidence of forensic expert Robert Collins Barnes, which linked Eastman to the murder scene.

The mistakes have already been found to have been unintentional, and Mr Adams was cleared of any wrongdoing by the inquiry into Eastman's conviction.

But Eastman's barrister Christopher Boyce, SC, argued he may use the stay application to mount more serious arguments about Mr Adams' failure to disclose the material.

That may require Acting Justice Whealy to rule on whether his old colleague engaged in prosecutorial misconduct or ethical breaches.

If that is proved, it could be used to help permanently prevent a second trial.

Earlier this year, Acting Justice Whealy refused to remove himself from hearing Eastman's stay application, saying he had had little to do with Justice Adams, and would not be required to make any judgments about his conduct during the time they spent together in the NSW Supreme Court.

But a full bench of the ACT Court of Appeal has now overturned that decision, ordering Acting Justice Whealy to recuse himself.

It agreed that the evidence of his contact and professional relationship with Mr Adams was "very thin".

"But this case is somewhat out of the ordinary," the judges wrote.

"The allegations of prosecutorial misconduct and ethical transgressions that are likely to be levelled against Mr Adams, and that [Acting Justice Whealy] is likely to be called on to decide, are very serious indeed."

It is unclear who will now hear the stay application.

All of the ACT's four full-time judges have had some involvement in the Eastman case in the past, likely ruling them outof hearing such proceedings.

Attorney-General Simon Corbell told Fairfax Media on Wednesday he would consider any requests for another acting judge, if made by the ACT Supreme Court chief justice.