Archaeologists working with traditional Aboriginal owners have discovered astounding evidence of the earliest human habitation of inland Australia.

A man answering a "call of nature" in Australia's Flinders made a chance discovery when he stumbled across the earliest evidence yet of human habitation in the country's arid interior.

Clifford Coulthard, an Adnyamathanha elder, was surveying gorges in the area in South Australian when "nature called". He happened across a rock shelter, which has turned out to be one of the most important prehistoric sites in Australia.

The site, known as Warratyi, shows that Aboriginal Australian occupied the country 10,000 years earlier than first thought - about 49,000 years ago, reported ABC Australia.

GILES HAMM The Warratyi rock shelter elevated above local stream catchment.

Coulthard, who is a co-author of a study about the discovery, said the findings weren't really a surprise to him.

"Our old people know we've been here a long time," he said.

Found 550 kilometres north of Adelaide, the shelter also contains the first reliably-dated evidence of human interaction with large or giant animals, known as megafauna.

GILES HAMM Giles Hamm inside the Warratyi rock shelter.

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Lead author Giles Hamm, a consultant archaeologist and doctoral student at La Trobe University, was with Coulthard when he found the site.

GILES HAMM/NATURE Sketches of the stone tools found inside the shelter.

"Nature called and Cliff walked up this creek bed into this gorge and found this amazing spring surrounded by rock art," Hamm told ABC Australia.

"A man getting out of the car to go to the toilet led to the discovery of one of the most important sites in Australian pre-history."

"Immediately when we saw that we thought, 'Wow, that's people lighting fires inside that rock shelter, that's human activity'," he said.

PETER TRUSLER An artist's impression of the diprotodon, a rhino-sized wombat-like megafauna.

They did not know at the time how significant their discovery was.

But, over the past nine years, Hamm and his colleagues worked with the Adnyamathanha people and recovered 4300 artefacts and 200 bone fragments from 16 mammals and one reptile from their excavations.

The archaeological treasures found in the shelter also include among the oldest-found examples of gypsum pigment, stone tools, and "earliest known use of ochre in Australia and south-east Asia".

Warratyi cave's astounding archaeological evidence

Seventy per cent of the bone fragments was likely to be from the yellow-footed rock wallaby, Hamm said.

The authors of the study, published on Thursday in Nature, said it finally settled the question of whether humans and megafauna overlapped chronologically.

"The idea there was no interaction between humans and megafauna has really been put to bed by the Warratyi evidence," said Lee Arnold from Adelaide University, one of the authors.

CREATING A PICTURE

By carefully matching the depth of the found artefacts with carbon dating and a secondary method known as "single-grain optically stimulated luminescence" dating of quartz grains, Hamm and his colleagues built up a picture of how frequently the shelter was used over nearly 50,000 years.

First usage was intermittent, with a 5000-year spike of bone remains and artefacts at about 40,000 years ago. Use declined from 35,000 years to about 24,000 years ago – a time when this part of Australia became "hyper arid", Mr Hamm said.

"We then see another spike in use from about 17,000 years ago," he said.

Hamm said when they first found the shelter they expected to find evidence of occupation from about 5000 or 6000 years ago.

"The first indication of its age was egg shells, emu shells from about 20,000 years ago," he said. They also found eggshell evidence of the presence of a large extinct megapode bird, "something like a huge Mallee fowl".

The find of a bone fragment from a diprotodon in the shelter was significant, said Gavin Prideaux from Flinders University.

"There is no way a diprotodon could scale to that shelter. It must have been brought there," he said.

Professor Sue O'Connor at the Australian National University, who was not connected with the study, said: "The methodology of this study is as good as it gets. It's a very important site and a really significant find."

However, she raised a question about how the findings dates were presented, using "mean calibrated years" rather than a probability of an age within a range of dates.

Connor said "everyone is keen to make their site sound older". However, she said her find of ochre at Carpenters Gap and this present discovery had "dates that overlap with our dates", while saying by email that "the Hamm discovery was likely older".

However, a more recent discovery she and Peter Hiscock at the University of Sydney announced this year of the world's oldest axe technology in the Kimberley included fragments of ochre, she said.

The age of that axe is within the same time span as that of the find announced on Thursday – between 49,000 and 46,000 years ago.

"We are finding new things all the time that shows how small our sample size is for this earliest period of human occupation of Australia," she said.

Hamm said there are clear gaps in our knowledge of the interior. How did people travel through the continent, he asked.

"It's likely they travelled along the great river systems: the Barcoo, the Thomson, Diamantina. But we clearly need to find d out more."

- Stuff, SMH