The federal government will strengthen commonwealth protections for Indigenous heritage sites in its long-awaited response to Rio Tinto's destruction of a sacred rock shelter at Juukan Gorge.

Environment minister Tanya Plibersek joined Minister for Indigenous Australians Linda Burney, Senator Pat Dodson and representatives of the First Nations Heritage Protection Alliance in announcing the reforms on Thursday, in response to the reports by the Joint Select Committee on Northern Australia into the destruction of Juukan Gorge, on 24 May 2020.

The Australian government has signed an agreement with the First Nations Heritage Protection Alliance to guide the reform process in the recommendations identified in the committee reports on Juukan Gorge.

The government has accepted seven of the eight recommendations and is in ongoing discussions with the Alliance on the eighth issue; whether ultimate responsibility for cultural heritage protection should sit with the Indigenous Affairs Minister or the Environment Minister.

The Minister said the new federal legislation would reflect free, prior, and informed consent; truth telling and open dialogue; and "genuine partnership – the kind that can only be entered into by equals".

Ms Plibersek thanked to Traditional Owners who participated in the inquiry.

"A particular gratitude is owed to the Puutu Kunti Kurrama and Pinikura people, who are the traditional owners of Juukan Gorge. I can only imagine how painful it was to give your testimony," she said.

"And I know how unfair it must have felt that it was us, as envoys from the state that allowed this destruction, who were asking you to relive your pain in public."

The Puutu Kunti Kurrama and Pinikura (PKKP) Aboriginal Corporation expressed anger and disappointment at the announcement in Canberra.

In a statement, PKKPAC chairman Burchell Hayes said the Corporation could not comment on the response because they had not been consulted on the content.

"All of this started with the destruction of our cultural heritage, everyone keeps on telling us they are sorry about it, but actions speak louder than words," Mr Hayes said.

"It seems like a media event in Canberra is more important than giving PKKP people the respect of asking us what can be done to try and stop something like the destruction of the Juukan rock shelters happening again, or even letting us know what the government is planning.

"We received an email on Tuesday 22nd November from the Minister's Office that this was happening with no detail or meaningful follow-up. We would have expected the Minister would want to meet with us before making a public announcement about our Country and cultural heritage. It is disappointing the media know more than we do."

Mr Hayes said the recent events confirmed that the PKKP peoples, not governments, had to look after themselves when it came to their country.

"We have tasted the devastation and we know what needs to be done."

Ms Plibersek's office later told ABC radio they had contacted the PKKPAC and offered a meeting with the Minister during the week.

At the official response launch the Minister said she understood why First Nations people "don't always trust the intentions of government or have much faith in our ability to listen and to learn".

"It is unthinkable that we would ever knowingly destroy Stone Henge, or the Egyptian pyramids, or the Lascaux Caves in France. When the Bamiyan Buddhas were destroyed in Afghanistan, the world was rightly outraged. But that's precisely what occurred at the Juukan Gorge," she said.

Ms Plibersek said the reports detailed "how we reached that shameful moment".

"(It's) important that Australians understand what happened. This was legal desecration. No laws were broken here. Instead, we had an entire system frustrating the interests of Indigenous history and culture."

The Minister said the reports exposed the national failure on protecting Indigenous cultural heritage.

"There were partnership agreements signed under gross inequalities of power, and that were only ever really understood by one party," she said.

"There were gag clauses, meaning traditional owners were not allowed speak out publicly without permission from Rio Tinto. There was a corporate culture that never took the company's obligations seriously… There were weak state laws."

She said the existing federal Aboriginal heritage legislation was designed as a last resort and was "confusing, difficult to access, and ultimately ineffective".