The study shows First Nations people suffered an estimated 93 per cent population loss in less than 80 years following the arrival of the First Fleet in 1788.
Frontier violence and disease contributed to that loss, with the present Indigenous population put at only 37 per cent of the pre-European estimate of 2.2 million people across Australia.
That compares with previous estimates of 250,000 to a million First Nations people.
Corey Bradshaw of Flinders University is part of a national research group working with Indigenous partners to investigate First Nations population through time.
Using computer modelling the researchers calculated the Indigenous population was up to seven times larger than previously estimated.
Researchers used three main approaches to calculate population, one being an archaeological one based on the discovery rate of archaeological artefacts that indicated population sizes, Professor Bradshaw told AAP.
The second technique used genetic data, looking at variations in modern Indigenous genomes to get an estimate of past population sizes.
The third technique involved researchers reconstructing the productivity of landscapes and how many people they could support, taking into account changes in vegetation over time based on ancient pollen and other records.
"When you look at those population densities and scale it up to the size of the continent we are well within ecological, genetic and archaeological evidence of how many people could have been here."
There was a suspicion that most of the previous historical-based estimates were vastly underestimating the size of the pre-European Indigenous population, Prof Bradshaw said.
"It was also wrapped up in a lot of racism at the time and built into the whole concept of terra nullius, that there's not a lot of people here so we can assume it's ours and take it over."
There was no incentive to count accurately, Prof Bradshaw said.
Colonialism, with its impacts of frontier violence against Aboriginal people, dispossession of lands and waters and deadly diseases like smallpox, led to great loss of life among Indigenous people.
Many of the deaths could be put down to "systematic massacres", Prof Bradshaw said, along with essentially genocide in Tasmania where Aboriginal people died of respiratory disease in concentration camps.
The researchers' modelling estimated just over two million excess deaths of Indigenous people occurred between 1788 and 1861 when only seven per cent of the estimated pre-colonial population survived.
Lead author Alan Williams, of James Cook University, said the findings highlighted the scale of demographic catastrophe experienced by Indigenous Australians due to colonisation.
They also showed the "remarkable survival, resilience and recovery" of First Nations people over the past century, Associate Professor Wiliams said.
Larissa Behrendt of the University of Technology Sydney, a Eualayai/Gamillaroi woman, said the findings were not about a marginal consequence of colonisation but told something extraordinary.
"Our survival is one of Australian history's most remarkable stories," Professor Behrendt said.
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