The immediate future of the Pastoralists and Graziers Association of WA has been clouded by revelations of 'serious financial misconduct' within the prominent farming lobby group.

An email on Friday to members of the PGA said membership payments were on pause and an investigation under way, with several staff of the 118-year-old organisation already stood down.

"The PGA executive and committee members have recently become aware of serious financial misconduct within its organisation," the email to PGA members said.

"The PGA has taken immediate steps to address the issues. As an organisation of long standing and credible reputation in the WA regional and rural community, the PGA is committed to focusing all its efforts in righting these issues.

The organisation vehemently opposed proposed changes to the state government's Aboriginal Heritage Act in 2023, which was repealed after ongoing controversy, confusion and consultation grievances from many stakeholders.

The influential farming body – which represents major agricultural players – suggested last month WA's proposed changes to renewing pastoral leases – which could entail Native Title compensation and Indigenous Land Use Agreements - could send many members broke.

Negotiated between the government and individual pastoralists, lease terms govern the use of the state's 85-million-hectare pastoral estate, with Aboriginal pastoral enterprises representing 31 per cent of that.

In late 2023 the government said its Aboriginal Pastoral Program would expand DPIRD's 26-year-old pastoral support program.

There is enormous potential to create a pathway to economic empowerment and self-determination through a thriving Aboriginal pastoral sector, it said at the time.

WA's Department of Planning, Lands and Heritage new lease renewal plan would include future potential Native Title compensation, and a requirement of renewed pastoral leases to negotiate an Indigenous Land Use Agreement, with leases across the state expiring between 2033 and 2065.

Although Native Title was not referenced in the proposed changes, a supporting DPLH document worried the PGA.

"[Pastoral] lease renewal triggers compensation to Native Title parties under the Native Title Act 1993," it read.

A WA government guideline to pastoral lease extensions also stated:

"Where Native Title exists or may exist, pastoral lessees will be required to negotiate an ILUA for the extension or regrant with the relevant native title party(s)."

PGA chair Ashley Dowden said in December an ILUA requirement could shift major financial obligations to members.

"If an ILUA is required to renew a pastoral lease it allows the Indigenous groups to hold pastoralists to ransom," he told the ABC in December.

Friday's bombshell email confirmed the agricultural lobby group's financial mishaps.

"[We] acknowledge there is a financial deficit in our current modelling, and are working hard to scope and rectify it," the PGA said.

"In the short-term, personnel within the PGA will be stepping aside.

"While the PGA works to develop an accurate assessment of its financial position, it asks for your patience and that you deal with facts, and not innuendo or rumour."

PGA president Tony Seabrook told the ABC's WA Country Hour on Friday the group had a financial deficit but would not be drawn on how much.

"It would be improper for me to start putting figures around that I can't verify," he said, adding he was conscious of implying misconduct while it was investigated.

"We've got a lot of records to go back through, and we are in the process [of doing that]… It goes back a very, very long time."