The woman herself was put on trial for making false accusations after she alleged the prison guard raped and seriously assaulted her in Canberra several years ago.

Their relationship had soured and the pair were locked in a bitter property dispute when the woman made the claims.

But a flawed police investigation into the allegations saw the man, who was a prison officer at the Alexander Maconochie Centre, charged and eventually remanded in custody.

He spent four months behind bars in Goulburn.

Police grew suspicious when the woman began to make allegations against her ex-partner's family.

She was put under surveillance, which police alleged showed she invented claims against the man's parents.

The prison guard also had an alibi for the alleged rape, which prosecutors were not told of immediately.

He was released and the charges dropped. His ex-partner was instead put on trial.

She was found guilty of five offences in the Magistrates Court but later launched a challenge against her convictions in the higher court.

The woman partly won an ACT Supreme Court appeal in August. The court upheld three convictions for public mischief.

But Justice Richard Refshauge overturned the woman's conviction for making a false accusation in the first alleged sexual assault on a technicality, after he found problems with the way some evidence linked to that claim was used.

He ordered she be acquitted. He upheld three convictions for public mischief.

The judge also set aside the conviction for the second false rape accusation due to problems with evidence, which he said amounted to a miscarriage of justice.

Justice Refshauge said he wanted to hear further submissions before he made orders about whether the woman should be acquitted or sent back to the Magistrates Court for a fresh hearing on the charge.

In a decision, published on Monday, Justice Refshauge said the woman should face a second trial in the interests of justice and due to the seriousness of the offence.

He noted the prosecution case was "not a weak one" and took into account the delay since the alleged offences, impact on witnesses and length of a fresh hearing.

The judge accepted the retrial would be stressful and difficult for the woman but did not find it would be oppressive.

"I am not satisfied that there is any disadvantage to [the accused] in a retrial of the charge nor that the complexity of the trial would be unfair, though it may be a challenge of conduct.

He ordered the case return to the lower court but said it should be heard by a different magistrate.

"I appreciate that the fragmentation of the charges and consequent sentencing should [the accused] be convicted is undesirable but the fair trial of the charges overrides that consideration."