The 13-metre skeleton, weighing a hefty 3.5 tonnes, has spent the past year buried in sand on a section of Gippsland's Ninety Mile Beach Beach between Woodside and Seaspray.

The adolescent male, which would have weighed about 30 tonnes, washed up last September and died soon after beaching itself.

While humpback whales are not a rare species, they have remained a missing piece of the museum's collection because undamaged specimens can be hard to reach.

''For a whale of this size to wash up on a beach with such good access is a real bonus,'' said Museum Victoria manager of preparations Peter Swinkels.

It took two days last year to strip the carcass back to a skeleton and break it up into manageable sections. Museum staff were able to remove 90 per cent of the meat and blubber. Internal organs were also removed and tissue and barnacle samples taken for the museum's molecular laboratory.

But there's only so much that can be removed manually. The rest was left to nature, with researchers burying the bones in sand so bacteria and other sea life could get to work.

The unusual cargo will arrive in Melbourne by truck. Before joining the collection it must be soaked in hot water, air dried and frozen to kill any bugs before being reassembled and going on display by mid-next year.

''The marine mammal collection has 1500 specimens, which makes it one of the largest in the southern hemisphere if not the world,'' said senior curator of mammals Kevin Rowe.

Whaling ceased on Australia's east coast in the 1960s, by which time the number of humpback whales had fallen to about 100. The population revived and there are now more than 8000 passing through Australian waters to breed.