Rio Tinto boss Jean-Sebastien Jacques will step down from his position as CEO following the the mining giant's destruction of 46,000-year-old rock caves at Juukan Gorge in Western Australia's Pilbara region in May.
Mr Jacques will remain in his role until the appointment of a new CEO, or until March 31, whichever is sooner.
Two other senior executives are also stepping down from their positions.
Chief executive, iron ore, Chirs Sailsbury and group executive, corporate relations, Simone Niven will both leave their positions by the end of the year.
The resignations come after calls for an overhaul of the mining company's executives and board.
The National Native Title Council (NNTC) has been calling for leadership change at Rio Tinto, this week writing a letter slamming the company's internal review into the destruction of the caves.
NNTC CEO Jamie Lowe told NITV News he welcomed the resignations but they should be seen as just the first step "in the right direction for things to change".
"It's significant I think, and the symbolic nature of it I think calls out other mining companies and says 'we mean business,'" he said.
"I think we've drawn a line in the sand, we've said 'enough is enough.'"
Mr Lowe said there needs to be further action and that he wanted to see Aboriginal leadership at Rio Tinto.
"We need an Aboriginal-led process to investigate the procedures and the culture within Rio Tinto that led to the incident - the explosion, blowing up the Juukan Gorge, and that's the only way we're going to see change happen within the organisation," he said.
"You get some Aboriginal leadership in there and they can drive the cultural shift."
For Mr Lowe said Indigenous people must be appointed to executive positions within Rio Tinto.
"We don't want another consultative group where they talk to Blackfullas and then go and get their mandate to do what they need to do," he said.
"We need Aboriginal people within decision-making positions at an executive and board member level.
"We also need, on the other side of that coin, Traditional Owners to be empowered through law and legislation to be able to have decision-making power on their Country.
"The only way cultural heritage should be able to be disturbed is with the approval of the Traditional Owners and in most states and territories, that power doesn't exist."
In a statement announcing the resignations of Mr Jacques, Mr Salisbury and Ms Niven, Rio Tinto chairman Simon Thompson said the company is determined to ensure the destruction of such "exceptional archaeological and cultural significance" never occurs again.
"We are also determined to regain the trust of the Puutu Kunti Kurrama and Pinikura people and other Traditional Owners," the statement said.
"We have listened to our stakeholders' concerns that a lack of individual accountability undermines the group's ability to rebuild that trust and to move forward to implement the changes identified in the board review."
Rio Tinto admitted in a submission to a Senate inquiry in August that it had three other options to expand its iron ore mine that could have avoided the destruction of the caves at Juukan Gorge.
Instead, it chose a fourth option to "access [to] higher volumes of high-grade ore".
The Northern Australia Committee, which is conducting the Senate inquiry into the destruction of the Juukan Gorge sites, also welcomed the resignations.
Committee Chair Warren Entsch said the evidence received at the inquiry made it clear that 'the internal culture at Rio Tinto was a significant factor' contributing to the destruction of the rock shelters at Juukan Gorge.
"New leadership, new structures and new operating principles within the company are essential to preventing such catastrophes in future," he said.
Following Rio Tinto's internal, board-led review, executives involved in the Juukan Gorge decision initially had their bonuses cut, amid mounting pressure for the resignations of some its most senior executives.