It isn't clear exactly what techniques the people living in the area at the time used to catch these fish.
Tuna can be caught using nets or by trolling hooks on long lines through the water, O'Connor said.
"Either way it seems certain that these people were using quite sophisticated technology and watercraft to fish offshore."
The site where the discoveries were made, known as Jerimalai cave, is a small rock overhang hidden behind in foliage, a few hundred meters from the shore.
"When I discovered it in 2005, I didn't think that Jerimalai would tell us about the very early occupation of Timor," O'Connor said. "I was quite surprised when I found all these fish bones and turtle bones."
So far, she and her colleagues have only excavated two small test pits at the cave, which contained a number of stone artifacts, bone points, animal remains, shell beads and fish hooks.
In just one of those pits, 1 meter square and 2 meters deep, they found 39,000 fish bones.
They also unearthed another rare find -- a small piece of fishing hook made from a shell, which dates to between 23,000 and 16,000 years ago.