Two of northern Australia’s most powerful Aboriginal land councils have been raided by the National Anti-Corruption Commission.

The Northern Land Council (NLC) in Darwin and Anindilyakwa Land Council (ALC) on Groote Eylandt were both targets of the commission this week as part of separate ongoing investigations.

The commission confirmed it had “carried out operational activity” in both Darwin and on Groote Eylandt in relation to ongoing investigations.

In a statement, acting NLC chief executive Jessie Schaecken said the corruption watchdog had “conducted a search warrant at NLC offices” on Monday and Tuesday.

“This was in relation to a report I made earlier in the year on suspicion of corrupt conduct of a former employee,” Ms Schaecken said.

“The NLC is committed to integrity and transparency, which is why I made the initial referral to the NACC.

“As this matter is currently under investigation it is not appropriate for me to make further comment.”

The NLC has not named the former employee at the centre of the allegations.

In June, the NLC was questioned during a Senate estimates hearing in Canberra over whether members of the land council had misappropriated COVID-19 stimulus funding.

At the time, Ms Schaecken said the NLC would investigate the allegations, however it remains unclear whether the corruption watchdog’s probe relates to those claims.

ALC boss sacked after corruption raids

The ALC’s offices on Groote Eylandt were also raided by the anti-corruption commission on Wednesday, amid an ongoing investigation centred on its former chief executive, Mark Hewitt.

The ALC's newly elected board held a meeting later the same day, after which Indigenous Australians Minister Malarndirri McCarthy confirmed Mr Hewitt had been removed from his role as the council’s chief executive.

"I received a letter from the ALC chair informing me that at its meeting on October 16, the ALC board resolved to terminate the employment of the ALC CEO," Senator McCarthy said in a statement. 

"Without the trust of the Anindilyakwa people and other key stakeholders, the ALC cannot properly achieve its mission of serving and advocating for the interests of the Anindilyakwa people." 

Mr Hewitt and the ALC have been contacted for comment.

Call for federal inquiry into land councils

In the wake of the raids, Victorian senator Lidia Thorpe reignited her call for a far-reaching federal inquiry into Australia’s Aboriginal land councils.

“Seeing land councils get raided like this only creates ammunition for them to be attacked and discredited, which undermines self-determination,” Senator Thorpe said.

“It's why I've been pushing for a parliamentary inquiry into this issue.

“We need to get to the bottom of the problems around these bodies to ensure they are truly representing the aspirations of First Peoples that they purport to represent.

“This will also help the broader community to trust and support the important role of genuine representation and self-determination.”

Senator McCarthy did not respond to questions about whether the government would back Senator Thorpe’s position.

In regard to the raids, she said “investigations by the National Anti-Corruption Commission are a matter for [it].”

“As Minister for Indigenous Australians, I expect strong governance and accountability from all land councils,” she said.