A parliamentary joint committee into the destruction of sacred 46,000-year-old caves by the major miner, has heard desecration of Indigenous fauna has occurred after the company announced sweeping changes to cultural engagement in 2020.

Greens senator Lidia Thorpe during the hearing said she had become aware of bulldozers running over dingo pups at a WA mine site, with traditional owners not being engaged to remove the animals to safe location.

"This has happened recently, and traditional owners requested that an environmentalist, be on hand at site for relocating animals before clearing land," Ms Thorpe said.

"This was ignored and the dingo pups were destroyed and squashed by a bulldozer."

The Canberra Times understands staff had engaged with Rio Tinto to remove a den of dingoes, but was ignored by the company.

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Rio Tinto chief executive of its Australian division, Kellie Parker said she was not aware of the situation, but any cultural issue would be forwarded to the general manager of the site, rather than the corporate board under the new framework, designed to ensure local Indigenous groups have direct contact with specific mines.

"It does sound distressing, and we will take that on notice and commit to an investigation," Ms Parker said in response to Senator Thorpe's question.

Ms Thorpe then replied: "I've heard a lot of reasons why you're sorry for destroying sites. But this has happened recently. What are you doing about stopping this behaviour of destroying our totems and country?"

Rio Tinto in a statement provided to The Canberra Times said it had not found any evidence of the claims made by Ms Thorpe during the hearing.

"We have checked with all of our mining operations across the country and, as it stands, have found no evidence to substantiate these claims," a company spokesman said.

In May 2020, Rio Tinto blew up a network of caves in Juukan Gorge to expand one if its Pilbara mines, but failed to consult the local Indigenous groups about the destruction of sacred sites.

Following the impact of the scandal, Rio Tinto announced a management and operating structure overhaul, which included the ousting of its chief executive at the time, Jean-Sebastien Jacques.

The London headquartered mining giant which is listed on the Australian stock market has also been criticised for a lack of Australian representation in senior management and on the board, despite the majority of mining operations being in Australia.

Following the departure of JS Jacques, Rio Tinto elected Jakob Stausholm as its new CEO, who is Danish.

Ms Parker was appointed Australian CEO after the Juukan Gorge incident.

It was also heard during the committee the Puutu Kunti Kurrama and Pinikura people affected by the cave destruction at Juukan Gorge had not yet received any form of reparations yet from the incident.

Rio Tinto confirmed discussions regarding reparations are ongoing.

"We have been working with the PKKP to firstly rebuild our relationship and ... and commit to the reconstruction of the gorge," Ms Parker said.

Following questions from Labor senator Patrick Dodson, it was also revealed Rio Tinto was involved in the destruction of Indigenous artefacts on two separate occasions in the 1990s.

Rio Tinto said its does not hold internal records of the "accidental disposal" event in 1995 and flagged the incident in 1997 had likely not considered the cultural significance of artefacts.

"We don't have any records to show that if this was communicated to additional owners or not," Ms Parker said.

"If we didn't communicate this to them at the time, we absolutely regret that."

Head of Indigenous affairs at Rio Tinto, Brad Welsh also said processes in the company today would prevent an event like this from occurring again.

"We do recognise that decisions made on the management of these materials may not have adequately considered archaeological and cultural values in the analysis completed," Mr Welsh said in relation to the 1997 incident.

"In today's processes, such analysis and decision making would be completed with traditional owners and with consistent methods applied across all materials."

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