Rio Tinto has written to Aboriginal traditional owners in the Pilbara promising to work with them “based on respect, transparency and mutual benefit” ahead of its second appearance at a federal parliamentary inquiry into the company’s destruction of a 46,000-year-old sacred site at Juukan Gorge in May.

The letter, sent to several traditional owner groups including the Puutu Kunti Kuurama and Pinikura peoples (PKKP), whose sacred site Rio Tinto obliterated, said the company knew it had “much work to do to rebuild the trust of the traditional owners on whose land we operate”.

Rio Tinto promised to “modernise” their agreements by “not enforcing” so-called gag clauses, which have prevented Aboriginal people from speaking publicly about the destruction of their heritage. It also pledged not to enforce clauses that would stop traditional owners applying for statutory protection of any cultural heritage sites.

PKKP Aboriginal Corporation told the parliamentary inquiry on Monday that in the nine days of “absolute hell” leading up to its destruction of Juukan Gorge, Rio Tinto warned them they were bound by such a clause and could not apply for a federal emergency halt to works without first asking Rio Tinto’s permission and giving 30 days’ notice.

“What we were reminded of by Rio’s lawyers was that we were not able to engage seeking out an emergency declaration that perhaps would have stopped proceedings, because of our claim-wide participation agreement,” the PKKP Aboriginal Corporation chief executive, Carol Meredith, told the inquiry.

The letter also commits the company to reassessing activities that have the potential to impact cultural heritage sites, and more regular consultation – especially when new information about the importance of a site is found.

Rio Tinto says it is considering the potential public release of its deals with traditional owners in the interests of greater transparency.

The content of the agreements Aboriginal people have signed with Rio and other mining companies has been under scrutiny at the inquiry. Legal experts expressed concerns that traditional owners may have contracted away existing rights under the law.

Greg McIntyre SC, an executive member of the Law Council and a leading native title barrister, told the inquiry there was “no real justification” for legacy agreements between mining companies and traditional owners to remain confidential.

Because the parties were not operating on a level playing field, the agreements should be revisited, he said, particularly where they may contain clauses that impinge on, or remove, other legal rights traditional owners might have.

“There should be statutory provision which prevents the contracting out of rights,” said McIntyre, who led Eddie Mabo’s legal team in the Mabo case from 1982-1992.

He agreed that native title bodies were under-resourced.

“Some [prescribed body corporates] can barely afford a phone,” he said.

Rio Tinto will appear before the inquiry on Friday for the second time – the first since its three senior executives stepped down over the company’s handling of the Juukan Gorge disaster.

BHP, meanwhile, has avoided a shareholder vote calling on the company to immediately stop mining that could “disturb, destroy or desecrate” Aboriginal cultural heritage sites, after it struck a deal with the First Nations Heritage Protection Alliance to commit to improved practices.

The Australasian Centre for Corporate Responsibility, which proposed the resolution, said the agreement was struck at the 11th hour, after the BHP chairman, Ken MacKenzie, became involved in negotiations with Aboriginal leadership.

“Our relationships with traditional owners are among the most important that BHP has,” MacKenzie said at the annual general meeting. “I look forward to our continuing partnership to deliver the commitments we have made together, and our shared objectives.”

The First Nations Heritage Protection Alliance confirmed the deal but said BHP “has a very long way to go in meeting best-practice standards in cultural heritage protection”.

The National Native Title Council, a member of the alliance, said BHP had committed to strengthen free, prior and informed consent in agreement-making and support federal and state cultural-heritage law reform.

The council’s chief executive, Jamie Lowe, said that was the first step for BHP on a very long journey towards best practice.

“Frankly, these commitments, though strongly welcomed, represent the very minimum expectations that should have been common practice in Australia decades ago,” Lowe said. “Mining companies and Australian governments have got a long way to go.”