The chair of a South West land council that struck the nation's biggest Native Title deal has denied deep conflict exists in the Noongar community over the rollout and delivery of a $1.3 billion deal it negotiated.

South West Aboriginal Land and Sea Council secured the deal - known as the Settlement - in 2021 after former WA Premier Colin Barnett proposed a settlement with the Noongar people of Perth and the south west of Western Australia following a stalemate in a lengthy Federal Court battle.

On Thursday it was reported the deal was in turmoil amid a power struggle between the South West Aboriginal Land and Sea Council (SWALSC) and six regional Aboriginal organisations established after the settlement to help manage the $1.3b, and allegations it secretly accessed emails of one of regional CEOs in August last year, supposedly raising concerns at the South West Council.

The landmark agreement had bipartisan support as it included a $600m future fund and 200,000sq km of land, which cleared roadblocks for farmers, developers and government and was seen as an economic boon for the Noongar people.

SWALSC chair Professor Dennis Eggington AM told National Indigenous Times on Thursday he was frustrated at the report in The Australian and was not surprised significant agreements involving recognition of Noongar people as Traditional Custodians of WA's South West could lead to disharmony and diverse opinions within the community.

"The South West Native Title Settlement is, in fact, proceeding to plan. Money is going into the Noongar Boodja Trust, the Regional Corporations are being funded and are developing their organisations, and SWALSC is providing core services to those corporations," he told National Indigenous Times.

He said it was not surprising for unrest to emerge when there were seven Aboriginal corporations in the structure.

"While many Noongars initially opposed the Settlement, after it was approved most Noongars got behind it and are trying to make it work," Prof. Eggington said.

"The article fixated on a single incident which happened over a year ago, in 2023. The incident was investigated early this year, and the results of the investigation were circulated to the Regional Corporations and other interested parties in May 2024.

"As a provider of core services to the Regional Corporations, SWALSC also serves as a central advocate for the Noongar Nation, working towards the overall benefit of Noongar People by bringing their professional experience and expertise into protecting, promoting ,and supporting Noongar culture, customs, languages and traditions.

"It accepts that improvements to the services provided at the start would need to occur. Throughout this evolution, a number of reviews have taken place to identify how to improve our services."

Mr Eggington said complaints against SWALSC were investigated and the council accepted the findings and modified its operation.

"We did this because we have a commitment to service improvement," he said, denying reports of deep problems within the organisation.

"All the issues raised have either been resolved or are in the process of being dealt with."

Mr Eggington said a SWALSC-commissioned independent internal audit report in response to complaints over its accounting service found "the accounting operations of the SWALSC are fit for purpose and functioning effectively in accordance with the Service Agreement".

He said claims lawyer Anthony Bevan was conducting an "inquiry into the South West Council's functions" gave an impression of disfunction or wrongdoing.

"Mr Bevan is undertaking the annual review of SWALSC required by the Noongar Boodja Trust deed," Mr Eggington said.

"We acknowledge that all organisations have detractors.

"While we are aware that a few people are still actively working to undermine the Settlement, we accept that as inevitable in the natural order of things.

"Our Noongar people remain committed to unification across Noongar boodja, and our focus is on continuing to build a robust and unified Noongar Nation supported by seven strong corporations.

"We remain committed to working with all Noongar people and the Western Australian government, to ensure the successful implementation of Australia's biggest native title deal, which we believe is in the best interest of the Noongar community, and the broader state of Western Australia."