Rio was roundly condemned for its actions when it dynamited the sacred site to access iron ore lying underneath in spite of objections from the local aboriginal community.
Last month, the FTSE 100 mining giant stripped bonuses from Jacques, Chris Salisbury, the head of its iron ore division, and PR chief Simone Niven following an internal investigation into what happened.
Today, the miner said several significant shareholders had subsequently expressed concerns about executive accountability for the failings identified in the review.
Jacques, who is stepping down by mutual agreement with the board, will leave his role by 31 March 2021 at the latest or earlier if a successor is found, Rio said.
Chris Salisbury is also to leave at the end of 2020 along with Niven.
Simon Thompson, Rio Tinto’s chairman, 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.
"What happened at Juukan was wrong and we are determined to ensure that the destruction of a heritage site of such exceptional archaeological and cultural significance never occurs again at a Rio Tinto operation".
The ancient caves in the Juukan Gorge rock shelters were regarded as among Australia's most significant archaeological sites with evidence of human life dating back 46,000 years.
Rio Tinto repeated its pledge to establish a new Social Performance assurance function, reporting to Mark Davies, Group Executive, HSE, Technical and Projects, to strengthen oversight of communities and heritage practices.
No surprise says broker
“The big change at the top of Rio Tinto isn’t surprising given the miner was coming under sustained fire from all quarters over the way it’s handled the legal destruction of the historically important Jukkan rock shelters in Western Australia," said Susannah Streeter at Hargreaves Lansdown.
"The site was destroyed against the wishes of traditional owners and many shareholders had been mightily unimpressed with the findings of the internal review.
"Shaving short term bonuses for some senior executives just didn’t cut it in terms of an apology, and although CEO Jean Sebastian Jacques did eventually say sorry at an Australian senate enquiry, it was too little, too late.
"There will inevitably be concerns that the company will be rudderless in the meantime, but the board clearly believe a tarnished management team staying in place would be worse for the company in the longer term.”
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