Mining giant BHP Billiton is poised to destroy at least 40 – and possibly as many as 86 – significant Aboriginal sites in the central Pilbara region of Western Australia (WA) to expand its A$4.5bn (£2.4bn) South Flank iron-ore mining operation, even though its own reports show it is aware that the traditional owners are deeply opposed to the move.

In documents seen by Guardian Australia, a BHP archaeological survey identified rock shelters that were occupied between 10,000 and 15,000 years ago and noted that evidence in the broader area showed “occupation of the surrounding landscape has been ongoing for approximately 40,000 years”.

BHP’s report in September 2019 identified 22 sites of scattered artefacts, culturally modified trees, rock shelters with painted art, stone arrangements, and 40 “built structures … believed to be potential archaeological sites”.

Under section 18 of the Western Australian Aboriginal Heritage Act, the traditional owners – in this case the Banjima people – are unable to lodge objections or to prevent their sacred sites from being damaged.

They are also unable to raise concerns publicly about the expansion, having signed comprehensive agreements with BHP as part of a native title settlement. BHP agreed to financial and other benefits for the Banjima people, while the Banjima made commitments to support the South Flank project.

But the Banjima native title holders told the WA government in April they did not want any of the 86 archaeological sites within the project area to be damaged, saying the “impending harm” to the area “is a further significant cumulative loss to the cultural values of the Banjima people”.

Guardian Australia has seen correspondence from an archaeological adviser to the Banjima to the WA government in April this year in which they say they “in no way support the continued destruction of this significant cultural landscape” but “are equally aware” they cannot formally object to the section 18 application.

This letter in April followed one sent in December 2019 in which the native title holders said: “The significance of the sites impacted by the notice to Banjima people is such that Banjima people cannot and do not support the destruction of those sites as proposed by the notice as to do so would be inconsistent with their cultural obligations to protect those sites.” They would “suffer spiritual and physical harm if they are destroyed”.

They said they were “worried about the cumulative impact of so many sites being the subject of a single notice for destruction and that not one of the sites is deemed worthy of protection in situ by BHP”.

BHP’s 2019 report said “it had taken into account the views and recommendations provided by the Banjima representatives during the consultation and inspection” but decided it was “not reasonably practicable for BHP to avoid the eighty-six (86) potential archaeological sites” at the South Flank mine development area.

BHP suggested the areas could be excavated, salvaged or deconstructed but also noted the Banjima did not want any of the objects or heritage values within the 86 potential archaeological sites to be removed or relocated.

BHP also offered to engage “a suitably qualified expert to digitally capture the extent and form of each stone arrangement using DPGS [differential global positioning system] and drone footage, with a view of creating a three-dimensional computer model and video”.

“Any cultural material salvaged as part of these programs shall be stored in the cultural repository at the BHP Mulla Mulla Heritage Office until a different location is nominated by the Banjima people,” the company’s assessment report said.

All 86 sites identified in the BHP application were assessed by WA’s Aboriginal Cultural Materials Committee, which controls the protection of heritage, but only 40 were considered by the ACMC to meet the threshold required to be a protected heritage site, despite the Banjima saying all 86 should be protected.

BHP said ministerial consent for its section 18 application covered approximately 40 heritage sites.

“We speak regularly with the Banjima community and have reiterated our commitment to working closely with them through the lifecycle of the South Flank development to minimise impacts on cultural heritage,” a spokesman for BHP said.

The revelations follow the apology last week by the chief executive of Rio Tinto iron ore, Chris Salisbury, for destroying the rock shelter in Juukan Gorge, which was blown up in mining works at the Brockman 4 iron ore mine near Tom Price in the Pilbara region on 24 May, saying there had been a “misunderstanding” with traditional owners the Puutu Kunti Kurrama and Pinikura people.

On Tuesday, more than 300 protesters gathered in face masks outside the company’s offices on St George’s Terrace in Perth to call for Salisbury’s resignation.

Protest organiser Robert Eggington, a Noongar man, said Rio Tinto had exploited the weakness of WA’s 48-year-old Aboriginal heritage laws, which have been under review for two years.

“They used that against the people and then turned and blamed [it on] misunderstandings between the company and the custodians of that site,” Eggington said.

Rio Tinto received ministerial consent under the WA legislation to destroy the site in 2013. That legislation does not give traditional owners the right of appeal.

BHP has said the South Flank project will create around 2,500 construction jobs, more than 600 ongoing operational roles and generate many opportunities for Western Australian suppliers. The project is expected to produce ore for more than 25 years.

The Western Australian minister for Aboriginal affairs, Ben Wyatt, confirmed he approved the South Flank expansion on 29 May, three days after the destruction of Juukan Gorge made global headlines.

But he has urged BHP to cooperate with the Banjima under what are now “changed circumstances”.

“As with any agreement, some circumstances can change including the understanding of heritage values of particular sites.

“I urge parties to such agreements to cooperate on management of those changed circumstances.

“I have asked BHP to work with Banjima to do what it can to avoid or minimise the impact on this site, regardless of the section 18 approval.”

Wyatt said impending reforms to the WA Aboriginal heritage legislation will end the section 18 process and reinforce the need for land users to negotiate directly with traditional owners.

Wyatt said he wants to see impacts to Aboriginal sites “limited to the practical extent possible” but that he is “cautious about governments interfering in private negotiations by registered native title holders”. 

Companies such as BHP make significant investment decisions on the basis of these agreements with native title groups, which in turn generate substantial benefits, he said.

“Our first principle is to seek to avoid impacts to cultural heritage, through planning and ongoing consultation with traditional owners. This approach is supported by the individual land use agreements we establish in partnership with traditional owners, and is in addition to meeting the requirements of Aboriginal heritage protection laws” a BHP spokesman said.