Australia's largest Indigenous legal organisation has apologised "without reservation" to ousted chief executive, Priscilla Atkins.

The apology by the North Australian Aboriginal Justice Agency (NAAJA) was published on its website on Wednesday morning, and comes after a judge ruled in June Ms Atkins had been unlawfully sacked after she had raised allegations of misconduct amongst senior members of staff.

Justice Charlesworth ruled NAAJA contravened the Fair Work Act when they took adverse action against Ms Atkins on six occasions.

She said NAAJA failed to prove they did not take this action because she exercised, or threatened to exercise, her workplace rights, and it was therefore presumed to have acted for these unlawful reasons.

Justice Charlesworth also found the NAAJA board acted unfairly when instigating an independent audit targeting Ms Atkins, after she had put forward corruption allegations against finance chief Madhur Evans.

In a statement, NAAJA said they "unequivocally accepts the findings made by the Court".

"NAAJA apologises without reservation to Ms Atkins for the unlawful action it took against her and the hurt, pain and suffering she endured as a result of those actions, as well as any damage suffered to Ms Atkins' reputation by reason of NAAJA's actions," a spokesperson said.

"NAAJA sincerely hopes to move forward from the events of the past two years in a professional and cooperative way with Ms Atkins for the benefit of Ms Atkins, NAAJA and the community that NAAJA proudly serves."

The court heard Ms Atkins argued she was terminated from NAAJA after accusing Ms Evans of making discrete payments to then-chair Colleen Rosas, as well as bullying employees, recording conversations with employees non-consensually, and disclosing confidential company information.

When Ms Rosas heard these accusations, the court was told she accused Ms Atkins of securing her long-standing chief executive position for another five years by forging her signature on the extension document.

NT Police concluded an investigation into Madhur Evans last year with no adverse findings.

Ms Atkins was suspended from her role in November 2022 after allegations by Ms Rosas and NAAJA employed BDO - an external auditor - to oversee the conclusion of the investigation.

The report was critical of Ms Atkins, who has always denied the contents of BDO's findings.

However, Justice Charlesworth criticised the constrained nature of the audit, arguing Ms Rosas withheld information from BDO which resulted in their investigation being deliberately confined.

She found Ms Rosas had deliberately withheld information from the audit, which was "not consistent with a genuine desire" for the audit to be fair and make factual findings.

It was a "curious feature of the case" that only after she was fired did the board ask Ms Atkins for a response to the BDO findings, Justice Charlesworth said.

Ms Rosas remains as NAAJA's deputy chair.

Justice Charlesworth said the letter to Ms Atkins, advising her of her dismissal in February 2023, was "purporting to afford her procedural fairness in connection with a decision that had in fact already been made".

"The evidence does not support a conclusion that the few directors involved in that activity had a genuine desire to afford Ms Atkins procedural fairness," Justice Charlesworth said.

On Wednesday, NAAJA confirmed Ms Atkins remains chief executive. This, despite the organisation having gone through six acting chief executives in 18 months.

"For the avoidance of doubt, her [Ms Atkins] employment is not subject to any suspension or ongoing disciplinary investigation," the NAAJA spokesperson said.

"NAAJA wholly resiles from any express or implicit findings of wrongdoing made by it against Ms Atkins in the lead up to her purported and unlawful dismissal."

In August, the legal organisation set about restructuring their operation in the wake of a trouble-plagued 18 months, including the stepping-down of board chairman Hugh Woodbury—who was appointed despite NAAJA knowing he previously pleaded guilty to assaulting his then-pregnant partner.

At least four directors stood down from the NAAJA board at the same time.