Traditional owners who lost hundreds of artefacts and haven’t been paid royalties under a deal brokered between the Western Australian government and Rio Tinto in the early 1990s say the mining company should face a judicial inquiry.

The federal parliamentary inquiry into Rio Tinto’s destruction of the 46,000-year-old Juukan Gorge rock shelters held its final public hearing on Friday.

The last to give evidence, Rio Tinto’s Australian chief executive, Kellie Parker, and Indigenous general manager of operation, Brad Welsh, told the inquiry the company had undergone significant change since the inquiry began last year.

Parker used the hearing to publicly apologise to the Eastern Guruma people for the destruction of hundreds of artefacts that were salvaged from Rio Tinto’s Marandoo mine in the 1990s, sent to Darwin to be studied, and ended up in a rubbish dump.

Consent to salvage the materials was granted by the WA government in 1992 under the Aboriginal Heritage Act, the same legislation used to approve the destruction of Juukan Gorge.

Management of the mine was authorised under a separate act of parliament, the Marandoo Act 1992, which meant the Eastern Guruma people were unable to mount any legal challenges and also do not receive ongoing royalties.

“I acknowledge that the events of Marandoo, including the passage of the act, the disposal of salvaged materials, and the reduced access to country have all caused hurt and pain for Eastern Guruma traditional owners,” Parker told the hearing.

“I reiterate our apology to the Eastern Guruma and confirm Rio Tinto is committed to working with them to support the repeal of the Marandoo Act, modernise our agreement to meet our shared expectations of partnership, and do our best to heal the wounds of the elders and the Eastern Guruma people.”

Liberal senator for Western Australia Dean Smith asked why Rio should not face a judicial inquiry for its actions, comparing it to the decision to call a judicial inquiry into Crown casino in Perth after it had lost its social licence to operate.

Parker said the company had “transparently” provided information to the parliamentary committee, and was “changing our business, not only in the way that we do business but the work that we do with traditional owners and how we protect cultural heritage”.

Tony Bevan, a director of Wintawari Guruma Aboriginal Corporation, which represents the Eastern Guruma people in the Marandoo agreement, said Rio had also lost its social licence and should face a judicial inquiry.

“They should face a judicial inquiry just so they can be compelled to answer the questions, because there’s quite a few questions today that they did not answer,” Bevan told Guardian Australia.

The Marandoo artefacts were sent to the Northern Territory University, now Charles Darwin, and disposed of in 1995 and 1997. The committee heard the university had not responded to an invitation to give evidence.

“It appears from our records that we at Rio Tinto have become aware of the disposal after the fact, and on becoming aware of the disposal Rio Tinto should have communicated this directly to the traditional owners,” Parker said.

“We don’t have any records to show if this was communicated to traditional owners or not. If we didn’t communicate this to them at the time, we absolutely regret that. But we also haven’t identified any evidence that there was a deliberate decision to withhold such information from Eastern Guruma people.”

Welsh said artefacts salvaged were reviewed by archeologists from Northern Territory University prior to being destroyed, and that the material destroyed appears to have been determined to be “non-artifactual”.

He added that Rio still holds 500 sample bags full of artefacts belonging to Eastern Gurruma people.

“The large number of types of materials that have been retained, and the subsequent research on these, suggest to us that significant efforts were made to salvage items of cultural value,” Welsh said.

The Labor senator for Western Australia Patrick Dodson asked Parker if Rio agreed that the principle of free, prior and informed consent, which is a core principle of the United Nations declaration on the rights of indigenous peoples, should be included in Australian laws governing the protection of cultural heritage. He also asked if Rio believed native title holders should have an exclusive right to determine whether their sacred site can be destroyed or not.

Parker said Rio “continues to strive to achieve free, prior and informed consent of Indigenous communities and we’ve learned a lot since Juukan”

She also said the company “recognises that traditional owners are the only people who can determine cultural significance”.

Dodson said neither response really answered the question.

Parker also said Rio Tinto had begun talking to Reconciliation Australia, which severed its relationship with the mining company after it destroyed Juukan Gorge against the wishes of the traditional owners at the start of reconciliation week last year, to see how they might repair the relationship.

“We recognise that not only did we break trust with Reconciliation Australia, we very much damaged their program that has been going for 20 years through our actions and particularly the timing of our actions,” Parker said.

The committee is due to file its final report by 18 October.

Guardian Australia understands the WA government is aiming to have its updated Aboriginal heritage laws through parliament by then, with the drafting process pushed along by the premier’s office.

The laws have been met by extensive protest from traditional owner groups in WA, who say there has been a lack of consultation and the new laws will be unworkable and not offer any further protection.

The draft legislation was unanimously rejected at the Yule River meeting, an on-country gathering of traditional owners in the Pilbara, on Thursday. The Aboriginal affairs minister, Stephen Dawson, declined to attend.

“It should be consulted with Aboriginal people, but the government wrote it without us. We want to write it with them,” said Doris Eaton, a Njamal and Pitjakarli elder and co-chair of the Yamatji Marlpa Aboriginal Corporation.

“Ask us, not tell us, what we want. We have no say, the government have the first and last say.”