Indigenous Affairs Minister Ken Wyatt says no Aboriginal site should ever be damaged by mining, but another could be on the block.

Mining giant Rio Tinto recently destroyed a set of ancient West Australian caves dating back 46,000 years, despite knowing for several years that the site was hugely significant to local Indigenous groups.

Mr Wyatt says it is not good enough, and has flagged an urgent review of state and federal heritage-protection laws.

“No site should ever be damaged. When I spoke with the traditional owners, one of them was explaining to me the absolute cultural relevance both those caves had and the destruction of them is like destroying the heart of the community,” he told ABC News.

But reports in the Sydney Morning Herald suggest Mr Wyatt is about to rule on the potential destruction of a 60,000-year-old Pilbara heritage site sitting squarely in the path of a mine.

Fortescue Metals Group (FMG) is planning to expand its Queens mine, which is part of the Solomon project. The project’s giant footprint covers dozens of heritage sites, including rock shelters, campsites and rock paintings, engravings and a 60,000-year-old rock shelter.

Eastern Guruma traditional owners have permission to excavate and investigate the sites' cultural values, but FMG reportedly sought a Section 18 consent from Mr Wyatt to destroy the first batch of sites before the investigations commence.

This forced the Aboriginal corporation to rush out and complete brief and urgent excavations at two of the sites. They discovered that the sites ran even deeper than anticipated.

“When you have a cave that people were living in 40,000-50,000 years ago ... over those years the deposits built up slowly and ground surface rises,” said archaeologist Kathryn Przywolnik, who is heritage manager at Wintawari Guruma Aboriginal Corporation which represents the Eastern Guruma people.

“So as we excavate the younger stuff is at the top and the older stuff is at the bottom. A shallow deposit suggests a lesser age and a deeper deposit can indicate a much older age.”

Testing of stone tools and other matter has revealed that the rock shelters have been used and occupied by humans as far back as 47,800 years ago in one cave, and approximately 60,000 years in another.

There is also evidence of rock engravings depicting animal and human figures, animal tracks and geometric motifs that are described as “sacred texts”, because they represent major Dreaming narratives in the area.

Dr Przywolnik said it is one of the most significant sites in Australia.

“When you find sites that are more than 40,000 years old you are getting into a very unique part of the Australian Aboriginal story,” she said.              

The archaeologists and the Eastern Guruma people have made submissions to the Aboriginal Cultural Materials Committee, calling on Mr Wyatt to protect 30 of the sites in the mine expansion footprint.

Fortescue chief executive Elizabeth Gaines says the company has an objective to ‘avoid’ culturally significant sites.

A spokesperson said Aboriginal Affairs Minister Ben Wyatt has not received the recommendations from the committee yet, but that “ordinarily the Minister accepts the advice from that statutory committee”.