Australia's largest Indigenous legal organisation has reached a settlement with their former chief executive, two-and-a-half years after she was "unlawfully sacked" from her position.

In a statement on Monday morning, the North Australian Aboriginal Justice Agency (NAAJA) said they had come to a confidential agreement with Priscilla Atkins, which would see the former chief executive officially resign from her position.

"We are pleased to have resolved this matter in a way that allows both NAAJA and Ms Atkins to move forward," NAAJA chairperson, Theresa Roe, said.

"While the legal process has been difficult, we believe the settlement provides a constructive resolution for all involved."

Last year, the Federal Court found NAAJA's board had acted unfairly when instigating an audit of Ms Atkins after she levelled corruption allegations at finance chief Madhur Evans.

Ms Atkins argued she was terminated after she accused Ms Evans of making discrete payments to then-chair, Colleen Rosas, bullying employees, recording conversations with employees non-consensually, and disclosing confidential company information.

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

Ms Evans was ultimately not found guilty of any wrongdoing, with NT Police making no adverse findings against her or Ms Rosas.

Ms Atkins was suspended from her role in November 2022 and NAAJA employed BDO - an external auditor - oversaw the conclusion of the investigation.

The resulting report was critical of Ms Atkins, who has always denied the contents of BDO's findings, and she was sacked in February, 2023.

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

She noted it was a "curious feature of the case" that it was only after she was fired did the board ask Ms Atkins for a response to the BDO findings.

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

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.

In a statement in November, NAAJA said they "unequivocally" accepted the findings.

"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.

The resulting confidential agreement between Ms Atkins and NAAJA likely draws a line under a saga which has caused reputational damage to the organisation.

After the court placed an injunction on hiring for Ms Atkins' replacement, NAAJA went through six acting chief executives in less than two years. Former acting deputy chief executive, Leeanne Caton - who stood down in June after only five months in the role - began circulating a petition in August among current and former NAAJA staff calling for a vote of no confidence in the board.

The legal organisation set about restructuring their operation, 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.

In November, NAAJA members approved a new constitution, opening membership to all Indigenous people in the NT, as well as reducing the number of directors from 16 to a maximum of eight, with, for the first time, three independent specialist directors joining five community directors.

Board members Carol Dowling, Bobby Wunungmurra, Theresa Roe, and Joyce Taylor were joined last week by independent directors David Parsons SC, Karl Dyason and Dominic McCormack.

"Since August 2024, NAAJA has provided legal representation to all Aboriginal people in criminal courts across the Northern Territory, unless they choose not to instruct NAAJA or there is a conflict of interest, and 82 per cent of NAAJA's Throughcare clients from 2024 have not reoffended when released from prison," a NAAJA spokesperson said.

"NAAJA is focussed on its objective of delivering high quality legal and support services to Aboriginal people in the Northern Territory."

The organisation said they will soon begin recruitment for a new chief executive.