Governance issues have yet again plagued the North Territory's biggest Indigenous legal organisation.

The North Australian Aboriginal Justice Agency is on the hunt for a sixth CEO in 18 months after acting chief executive Phil Brown resigned.

He advised the NAAJA board and NT Attorney-General's department of his decision earlier this month, The Australian reports.

He was the agency's fifth CEO in just 18 months, as the embattled organisation faced a string of upper management issues and public controversies.

Mr Brown is the nephew of NAAJA deputy chair Colleen Rosas, who the Federal Court found late last month had engaged in corrupt behaviour when, as acting chair, she sacked former CEO Priscilla Atkins.

Justice Natalie Charlesworth ruled in late June that NAAJA acted unfairly when instigating an audit of Ms Atkins after she levelled corruption allegations at finance chief Madhur Evans.

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

"The court is satisfied that each of the actions taken against Ms Atkins meets the description of adverse actions as defined in the Fair Work Act," Justice Charlesworth said.

It was accepted the resolution for Ms Atkins' termination was not made in compliance with the legal organisation's constitution, as per the claims of Ms Atkins.

"NAAJA's argument the resolution was valid, notwithstanding that noncompliance, is rejected," Justice Charlesworth said.

Ms Rosas has denied any allegations of wrongdoing.

Mr Brown's resignation is another blow to the embattled legal service, which was criticised for appointing incumbent chair, Arrernte man Hugh Woodbury – who replaced Ms Rosas earlier this year – despite being aware of his previous domestic violence charge against his pregnant partner.

There were also revelations the NT government was attempting to recoup almost $2.7 million in unspent funds for the 2022-23 financial year.

A mass exodus of staff at the agency last year forced it to suspend services in Alice Springs for six months.

Lawyers and politicians have repeatedly called for the agency's board to be replaced entirely as the controversies emerged.

A NAAJA spokesperson told National Indigenous Times that Mr Brown "has advised the board and the Attorney General's Department of his decision to not renew his contract next month due to family reasons".

"Mr Brown intends to continue in the role until a replacement is appointed to ensure that there is an orderly transition," they said.

"The board is going through a recruitment process to appoint a replacement acting CEO.

"Mr Brown has done a commendable job leading NAAJA and the board thanks him for his invaluable contribution."

The Federal Court last year put an injunction on the board, preventing it from hiring a permanent CEO amid the unfair dismissal case of Ms Atkins.

NAAJA this month appointed Matthew Connop as acting deputy CEO, replacing Leanne Caton, who made a surprise departure last month.

Mr Brown replaced outgoing CEO Darryl Pearce in February.

Ms Rosas said at the time that his exit was a natural end to his three-month contract, however weeks earlier Mr Pearce said he would "stick around for as long as they want me".

Mr Pearce had replaced Olga Havnen, who resigned after three months as CEO, claiming the NAAJA board needed to be removed immediately.

She had replaced John Paterson, who lasted six months, after standing in for long-time CEO Ms Atkins, who was ousted in late 2022, sparking the unfair dismissal dispute in the Federal Court.

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

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

In an earlier statement NAAJA said it would review the Federal Court's findings.

"NAAJA maintains a strong view that the board was justified in its decision to seek to terminate the employment of the former CEO and, as a result, we are surprised and disappointed by today's decision," a NAAJA board spokesperson said in a statement.

"We will review (the) judgement and seek legal advice regarding our next steps."