Dr Julien Louys of the Australian National University (ANU) School of Culture, History and Language, who led the project said these are the largest known rats to have ever existed.
"They are what you would call mega-fauna. The biggest one is about five kilos, the size of a small dog," Louys said.
"Just to put that in perspective, a large modern rat would be about half a kilo," said Louys.
Louys said the earliest records of humans in East Timor date to around 46,000 years ago, and they lived with the rats for thousands of years.
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"We know they're eating the giant rats because we have found bones with cut and burn marks," he said.
"The funny thing is that they are co-existing up until about a thousand years ago. The reason we think they became extinct is because that was when metal tools started to be introduced in Timor, people could start to clear forests at a much larger scale," said Louys.
The information can then be used to inform modern conservation efforts, researchers said.
"We're trying to find the earliest human records as well as what was there before humans arrived," Louys said.
"Once we know what was there before humans got there, we see what type of impact they had," he said.