Picked up by a commercial fishing vessel from more than a kilometre beneath the surface, the 65-centimetre section of skull once belonged to a beaked whale the size of a large dolphin.

Museum Victoria palaeontologist Erich Fitzgerald said though missing the rear end of the skull and the lower jaw, the fossil was significant because most marine fossils in museum collections were from shallow coastal rocks on the continental shelf.

This means that scientists know a lot about the marine life close to shore, with many deep-sea creatures remaining a bit of a mystery.

''The beaked whales are particularly enigmatic as they rarely come to shore,'' he said. ''They are the most poorly known group of whales,'' he said.

Some species of beaked whales are known to live in waters up to two kilometres deep.

Considered the second-most diverse group of whales, there are at least 20 known species of beaked whales. However, Dr Fitzgerald said there were likely to be many more, with new species still being discovered.

It is not yet clear what species of beaked whale the fossil belonged to - or even if it might be an extinct species.

The age of the fossil is also still to be established, with museum scientists testing the sediment found attached to the fossil and analysing its mineral composition.

Dr Fitzgerald estimated the fossil was less than 10 million years old - which would fall within an evolutionary important time for whales when many species began diverging.

''If we want to understand the history of the living species of beaked whale, we need species from that window of time because it's within that five to 15-million-year timeframe when it's thought that a lot of the living species started to split off from one another.''

The fossil was discovered by the FV Austral Leader 2 while fishing for Patagonian toothfish near Heard Island, a volcanic island that is part of Australian territory, 4000 kilometres south-west of Perth.