It is time for Australia to face the truth about hundreds of Aboriginal prisoners who died on Rottnest Island in the 19th century and are buried in unmarked graves, a leading Aboriginal academic says.

WARNING: This story contains images of Aboriginal people who have died.

Len Collard is a Whadjuk Noongar elder and professor of Aboriginal studies at University of Western Australia.

He has called for a more honest narrative about the jailing of 4,000 Aboriginal men and boys on Rottnest Island between 1838 and 1902.

The prison began as a "bold experiment" to give Indigenous offenders more freedom from confinement but became the centrepiece of a criminal justice system designed to crush any resistance to the spread of white settlement around the state, Professor Collard said.

"Rottnest became a prisoner of war camp where the patriots were chained up and removed from their country, from not only here in the Whadjuk lands but right across Western Australia, brought here to be imprisoned and do their time for whatever the allegation was," he said.

Aboriginal prisoners were made to work on Rottnest Island. ( Supplied: State Library of WA )

"I'm not saying the people were innocent, but the problem is we only have the policemen's word in the literature.

"People didn't even know what they got charged with, they couldn't speak the language, so how were they supposed to understand what was going on?"

Resort built over prisoners unmarked graves

In 1987, writing for The West Australian newspaper, I revealed the existence of a mass burial site underneath the island's Tent Land.

It had been discovered by workmen connecting services to the island's new golf course in 1962 and, although reported to state authorities, it was never made public.

Reporter Sean Murphy has followed the developments on Rottnest Island for 30 years. ( Supplied: Sean Murphy )

It took until 2007 before the Tent Land was closed down after ground-probing radar confirmed the remains of about 370 prisoners.

Professor Collard said the slow progress on properly commemorating the site was indicative of Australia's ambivalence about its Aboriginal history.

"Do patriots deserve better? Do the men that stood up to defend the nation, the first ones?" he asked.

"We're pushing this big narrative, militarising our history, lording the great battles that Australians gave their lives in. Well here [are] Australians ..., they gave their life."

"If we're going to patronise the ANZACS, and so we should, well then we need to do something better about Rottnest."

In May next year, the island resort lease expires and the original prison quod will no longer be used as hotel accommodation.

Elders, lore-men and women, as well as young people from the communities which had members imprisoned on Rottnest, will be invited to the island for a cleansing ceremony and to discuss the future use of the heritage-listed structure.

The original prison quod will no longer be used as hotel accommodation after May 2018. ( ABC News )

The Rottnest Island Authority's Aboriginal heritage officer Ezra Jacobs-Smith said a significant memorial would also be developed on the prison burial ground.

"Obviously all of this stuff we're doing on the island has those strong themes of truth telling, healing and reconciliation," he said.

"You can't have reconciliation without telling the truth and going through that healing process first and that's something we haven't done yet.

"So, the Rottnest Island Authority are keen to progress that reconciliation journey as much as we possibly can."

WA's Minister for Aboriginal Affairs, Ben Wyatt, said the proper commemoration of the burial site would be a historic and profound act of reconciliation for the state and would enhance Rottnest as a place to visit and enjoy.

He said Wadjemup, which is the traditional Noongar name for Rottnest, was a place of great significance and distress for Aboriginal people.

"Wadjemup's history should be known to all Western Australians," Mr Wyatt said.

"An honest reflection on historic Government policies — including those that had a devastating impact on our Aboriginal community — should be critically reviewed and discussed."

A memorial to 'help people understand what happened'

The Wadjemup Working group is helping design a culturally appropriate memorial on the burial ground. ( Supplied: State Library of WA )

The Rottnest Island Authority has been taking advice from the Wadjemup Working group, a five-member committee with representatives from the South West, Pilbara and Kimberley, which is helping with the design of a culturally appropriate memorial on the burial ground.

Committee member Barbara Bynder said her personal opinion was that proper recognition of the site was long overdue.

"It should have been done years ago but a lot has changed in 30 years," she said.

"Australians are now much more open to dealing with the Aboriginal history of Rottnest."

She said it was important that the memorial not be politicised and that it reflected the diversity of the communities where the prisoners came from.

"The reality is that Rottnest is a holiday destination, it's not about preventing people from going to Rottnest, it's about creating some sort of a memorial, to make people aware that it's a cemetery, a burial ground, that it's a place of importance and to reflect," Ms Bynder said.

"I want a memorial built on that site, so that people understand what happened here, its true history, so that all Australians can recognise and acknowledge it in a positive way, it's about walking together."