If the two species came together at the same place and time it could explain the hobbits' extinction.
An international team of scientists uncovered the remains of a previously unknown species of small-statured human, Homo floresiensis, in Liang Bua cave in 2003.
Known as "hobbits" after the characters invented by Lord of the Rings author JRR Tolkien, the creatures were originally thought to have lived as recently as 12,000 years ago.
Later experts dated the bones at between 190,000 and 60,000-years-old, while the most recent hobbit stone tools were thought to be 50,000 years old.
Although they used stone tools, there is no evidence that the hobbits had mastered fire. The hearth remains found in the cave were most likely left by modern humans, scientists said.
Lead researcher Dr Mike Morley, from the University of Wollongong in Australia, said: "We now know that the hobbits only survived until around 50,000 years ago at Liang Bua.
"We also know that modern humans arrived in Southeast Asia and Australia at least 50,000 years ago, and most likely quite a bit earlier.
"This new evidence, which is some of the earliest evidence of modern human activity in south-east Asia, narrows the gap between the two hominin species at the site."
Fossilised remains of even smaller ancestral hobbits who lived on Flores 700,000 years ago have further persuaded experts that the creatures really were a distinct human species.
They suggest that hobbits evolved from an earlier type of human, Homo erectus, that became marooned on Flores long ago.
The new findings are published in the Journal of Archaeological Science.
