The white carcass was found at a Mallacoota beach in the state's East Gippsland region, near the NSW border, and is only accessible by water.
Victoria's Department of Environment, Land, Water and Planning (DELWP) have since allayed fears it is Migaloo, who has not been spotted for two years after losing his tracking chip.
"DELWP officers have examined images of the dead humpback whale at Mallacoota and have confirmed it is a sub-adult female. Migaloo is a male," regional agency commander Peter Brick said on Sunday.
"DELWP and Parks Victoria staff will be further assessing the carcass over coming days."
The dead whale's colour will form part of the department's assessment.
Humpback whale carcasses that have been in the ocean for extended periods of time have been known to lose their colour and appear to be white.
Whether dead or alive, whales are protected under the Wildlife Act and it is an offence for members of the public to interfere, take or possess parts of a dead one.
It is also an illegal for people or their dogs to be within 300m of a beached whale.
"I urge anyone in the area not to approach within 300m of the carcass," Mr Brick said.
Migaloo was first sighted in 1991 off Byron Bay, when he was believed to be between three and five years old.
His moniker means "white fella" in some Indigenous languages.
Photos showing a dark patch of skin under barnacles on the throat was another sign the whale wasn't Migaloo, Macquarie University wildlife scientist Vanessa Pirotta says.
"That indicates that was external skin because we have barnacles on the outer layer of these animals," she told ABC TV.
Dr Pirotta similarly warned the public to steer clear of the whale carcass as it could carry a number of diseases and attract predators like sharks.
"If you have an animal like this on a beach, 40,000kg potentially of blubber and whale, that could naturally as it is decomposing leak juices into the area," she said.
16°C