One of Western Australia's biggest Indigenous charitable trusts is confident it won't have to reimburse millions of dollars to BHP as the miner reevaluates its royalty payments after realising it had overpaid the organisation.

IBN Charitable Foundation is paid royalties from BHP's production at its Mining Area C (MAC) operation in the Pilbara, on behalf of three traditional owner groups, the Yinhawangka, Banjima and Nyiyaparli people.

IBN co-chair, Jeff Parnell, told National Indigenous Times the organisation and BHP had ongoing discussions over the past three years regarding the issue and he wasn't concerned at the potential to reimburse any funds.

The issue arose three years after BHP commenced production at its giant South Flank mine, adjacent to MAC, which is not part of the IBN agreement but falls within the broader Banjima native title determination.

However, royalty payments were made to IBN as the claim border runs through part of its mining pit, with MAC on one side and South Flank on the other.

Mr Parnell stressed to National Indigenous Times reimbursement requirements may not eventuate and, if they did, could gradually be paid over the decades-long period of the agreement between BHP and IBN, with little impact on his members.

Last year IBN was paid $47m in mining royalties but confirmed in its annual report last October that BHP had determined the payments were too large over an extended period, as the South Flank mine expands beyond the IBN determination area.

National Indigenous Times understands BHP is working with IBN and the representatives of the three Traditional Owner groups before determining whether it will seek reimbursement of those funds.

"BHP have notified IBN that they believe they have overpaid production payments under the MAC Agreement to IBN over a number of years," IBN said in its report.

"However at the date of this report, BHP have not been able to finalise the calculation of this amount or decided whether they will indeed seek to recover the funds."

BHP's WA Iron Ore business had underlying EBITDA (earnings before interest, taxes, depreciation and amortisation) of $US21.8 billion for the financial year ending 2022, and $US16.7b for the YE 2023.

Royalty payments to IBN from BHP were nearly $47m in each of the past two financial years under the MAC agreement, an increase from $26m in FY21 and $9.4m in FY20.

According to Business News, IBN's total assets have grown to $211m, making it one of the largest indigenous charitable trusts in WA.

The current dispute follows a renegotiation of the original royalties agreement between IBN and BHP in the 2010s.

At the time, BHP said beneficiaries were not satisfied with IBN's structure, while IBN's then chairperson Lorraine Injie said it faced "the continuing threat of litigation from BHP", the publication said.