Prehistoric humans living more than 40,000 years ago had mastered the skills needed to catch fast-moving, deep-ocean fish, a new archaeological find has revealed.

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In a small cave at the eastern end of East Timor, archaeologist Associate Professor Sue O'Connor from the Australian National University has unearthed the bones of more than 2,800 fish, some of which were caught as far back as 42,000 years ago.

She says the find shows the people living in the region had the sophisticated cognitive skills needed to haul in such a difficult catch.

Her findings appear this week in the journal Science.

"What the site has shown us is that early modern humans in island South East Asia had amazingly advanced maritime skills," she said.

"They were expert at catching the types of fish that would be challenging even today - fish like tuna. It's a very exciting find."

It is not clear exactly what techniques the people living in the area at the time used to catch the fish.

Tuna can be caught using nets or by trolling hooks on long lines through the water, Professor O'Connor said.

"Either way it seems certain that these people were using quite sophisticated technology and watercraft to fish offshore," she said.

Cave site

The site where the discoveries were made, known as Jerimalai cave, is a small rock overhang hidden behind foliage, a few hundred metres 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," Professor 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. But in just one of those pits, 1 metre square and 2 metres deep, they found 39,000 fish bones along with a number of stone artefacts, bone points, animal remains, shell beads and fish hooks.

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.

This is the earliest example of a fishing hook that has ever been found, the researchers say.

They are hopeful that more extensive excavations might reveal more hooks at the site.

"I think Jerimalai gives us a window into what maritime coastal occupation was like 40,000 to 50,000 years ago that we don't really have anywhere else in the world," Professor O'Connor said.