A prison building on Rottnest Island where thousands of Aboriginal men and boys were incarcerated will no longer be used as holiday accommodation.

It is a move welcomed by Noongar people as a significant step towards reconciliation and healing.

The island is a popular holiday destination off Perth's coast and famous for its pristine beaches and quokka selfie opportunities, but the failure to acknowledge its tragic history has long been a source of distress for Aboriginal people.

From Thursday, the 29-cell prison, known as the Quod, will close.

The Quod, the Rottnest prison that was built by and housed Aboriginal prisoners. ( 720 ABC Perth: Emma Wynne )

Aboriginal men were taken from all over Western Australia and imprisoned on the island from 1838 until 1904.

Aboriginal heritage officer Ezra Jacobs-Smith told ABC Radio Perth that around 4,000 men and boys, some as young as seven and as old as 80, were incarcerated in the Quod.

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They were put to work building houses, the lighthouse and roads that are still in use today.

"The people that were in charge at the time spoke about the prison on Rottnest as being a more humane option than being in prison on the mainland," Mr Jacobs-Smith said.

"They talked about it being a place where they might be able to rehabilitate them and teach them skills like farming.

"I think the reality didn't turn out to be that.

"I think we all agree now that it was more about control and the break-up of Aboriginal resistance to settlement across the state of Western Australia.

"A lot of the men that were taken away from country were significant male leadership in their communities."

Aboriginal prisoners on Rottnest Island, 1889. ( Supplied: State Library of WA )

Conditions under the first superintendent, Henry Vincent, were particularly cruel.

"A lot of men passed away because of the conditions they were housed in — dysentery, measles, influenza," Mr Jacobs-Smith said.

"There were severe beatings and five recorded hangings here; gallows were set up in the Quod and other prisoners forced to watch."

Future to be debated

Attention has now turned to what should happen to the Quod and the adjacent burial ground, which contains the remains of 370 Aboriginal people.

"I think the first step is recognising the truth of what happened here and to understand and respect this history," Mr Jacobs-Smith said.

"You can't imagine running a tourist business over somewhere like Auschwitz; that is the challenge that sits in front of us, the Rottnest Island Authority, the Aboriginal community and the wider community in WA who access the island quite regularly."

The Wadjemup Aboriginal Reference Group will now begin a thorough process of consultation to determine the site's future use.

Pamela Thorley is a member of the Wadjemup Aboriginal Reference Group ( ABC Radio Perth: Jo Trilling )

Group member Pamela Thorley said she was happy to see the Quod close.

"We have to consult widely across Western Australia and ensure that Aboriginal people who want to have a say on what happens here have that opportunity," she said.

"Ideas range from people who say 'burn it down', to people who say 'let's recognise it appropriately and have an interpretive centre'.

"Until we do the consultation and we do it properly, the answers are unknown."

The Rottnest Island burial site is believed to contain the remains of 370 Aboriginal men. ( 720 ABC Perth: Emma Wynne )

Some Aboriginal people have suggested the entire island, which Noongar people call Wadjemup, be handed back to the Wadjuk Noongar community, but Ms Thornley said that was not going happen.

Rather, she said she wanted to see Aboriginal people benefit from the State Government's plans to expand tourism and accommodation.

"I think there are lots employment training opportunities here for Aboriginal people," she said.

"I think there could be Aboriginal-owned businesses on the island, a ranger program, opportunities in hospitality, cultural enterprise.

"And we need to ensure that we have some type of memorial here telling the true history of the island."

Rottnest Island, which Noongar people call Wadjemup, will remain a holiday destination. ( 720 ABC Perth: Emma Wynne )

Ms Thorley expects it to be a long process but, if done well, could be an exemplary reconciliation project.

"This could be an international best-practice project.

"There's a lot of burden on us, the reference group, to ensure that it happens."

Until it does, visitors are encouraged to undertake a brief ceremony when they arrive to show their respect.

"Take a handful of sand and go down to the water and speak to the spirits," Mr Jacobs-Smith explained.

"We introduce ourselves and tell them who we are and why we are here.

"It's just a way of showing that respect and acknowledging what has happened in the past, and non-Aboriginal people are welcome to partake in that ceremony."