An Australian man searching for a toilet stumbled across the oldest-known evidence of Aboriginal settlement in existence.

The chance discovery happened while Adnyamathanha elder Clifford Coulthard was surveying gorges in the area and “nature called”.

He came across the arid site, known as Warratyi, which showed Aboriginal Australians settled there 49,000 years ago, 10,000 years earlier than previously thought.

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

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

"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 prehistory,” Mr Hamm told ABC.

"Nature called and Cliff walked up this creek bed into this gorge and found this amazing spring surrounded by rock art.”

Mr Hamm told how the pair noticed a rock shelter with a blackened roof and knew immediately it was a sign of human activity.

However, despite realising people had probably used the shelter to light fires, the researchers had no idea of the significance of their find.

For the past nine years, Mr Hamm and his team have recovered more than 4,300 artefacts from the one-metre-deep excavations, along with 200 bone fragments from 16 mammals and one reptile.

Co-author professor Gavin Prideaux also noted the discovery of bones from the extinct giant wombat-like Diprotodon optatum, and eggs from an ancient giant bird.

He also said the discovery was an important indication that humans may, after all, have been responsible for the extinction of megafauna.

"The find undermines one of the supposed pillars of support for climate change, not humans, causing the extinctions because the site shows humans lived alongside these animals and hunted them," he explained.

He also said his research paper, published in Nature, "smashed several paradigms about Indigenous Australians".

"People were set up in arid southern Australia by about 50,000 years ago and they had all these amazing technologies much earlier than what we've thought,” he said.

Previously, the oldest-known site in the arid zone, which accounts for roughly 70% of Australia’s land mass, dated back to 38,000 years and was found at Puritjarra in western central Australia.

"This discovery puts people moving south from the northern part of the continent to the southern interior a lot sooner than we thought," Mr Hamm said.

However, he also claimed the land was likely to have been less arid when it was occupied by the first settlers.

"In one sense they were trapped in the Flinders Ranges because once the climate changed [due to the last glacial maximum] it was too risky to move out of these well-watered ranges that had these permanent springs,” he said.

Michael Westaway, palaeoanthropologist at Griffith University, confirmed this theory and recently participated in a genomic study that found modern Aboriginal Australians are the descendants of the first people to inhabit Australia, and they had adapted genetically to survive in the desert.

"Our DNA paper suggested the arid centre at 50,000 years ago was not really a barrier to the movement of people, and this seems to be what Giles is suggesting — people were able to migrate south quite quickly," Dr Westaway said.

"There is a Eurocentric view that material culture in Australia is quite simplistic and backward, but this helps rewrite that story."

Mr Coulthard said he had worked near to the Warratyi site when he was a teenager and had been told of ancients shelters in the area.

However, he had forgotten the information and believes "the spirits showed me the road".

He said the Adnyamathanha people were proud and happy about the discovery.