News of the project sparked a public outcry on Thursday, prompting the company to announce later in the day that it would consult with Aboriginal groups before proceeding.
"We will not disturb the sites identified without further extensive consultation with the Banjima people," the company said in a statement.
"That consultation will be based on our commitment to understanding the cultural significance of the region," it added. "This will include further scientific study and discussion on mitigation and preservation."
The move follows the destruction of a 46,000-year-old Aboriginal site by rival Aussie miner Rio Tinto last month, which also received an angry public backlash.
It also coincides with a resurgence of the Indigenous rights movement in Australia in the form of widespread Black Lives Matter demonstrations calling for an end to discrimination.
BHP applied last year to work in an area, which includes 40 significant Indigenous sites as part of its 3-billion-dollar South Flank iron ore project -- with approval being granted by Aboriginal Affairs Minister Ben Wyatt.
Wyatt, who is himself Aboriginal, said at that time no objections were filed regarding the mines expansion and a comprehensive agreement was signed by BHP and the Banjima back in 2015.
"BHP agreed financial and other benefits for the Banjima people, while the Banjima made commitments to support the South Flank project," Wyatt said.
It is not yet clear how the consultation will affect the project which was due to begin production of iron ore next year.
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