H5 bird flu was detected for the first time in October on Australia's World Heritage-listed Heard Island, which sits some 4000km southwest of Perth.
Mainland Australia is free of the strain, which is present on all other continents and has devastated bird and animal populations.
Scientists who visited Heard Island estimated 13,359 southern elephant seal pups have died from the disease out of a total population of 17,364 - 76 per cent.
Their study, published in scientific journal BioRxiv on Wednesday, says the figure could be even worse as deaths were ongoing when their observations finished.
"It was very sobering but it was something that we were prepared for," Australian Antarctic Program senior research scientist Jarrod Hodgson said.
The strain was also found in king penguins, Gentoo penguins, Antarctic fur seals and a South Georgia diving petrel.
There was elevated mortality among king penguins and Gentoo penguins. There was also evidence of the disease at nearby McDonald Island.
The strain poses a severe and potentially catastrophic threat to the wildlife of the Southern Ocean because of their large, dense breeding habits, the study says.
Elephant seals and albatross were at particular risk given their low reproductive rates and late maturation, meaning population losses cannot be quickly recovered.
It is believed the strain first arrived on Heard Island in August, likely via infected wildlife from Crozet Islands some 1700km away.
Heard Island and McDonald Islands are a haven for wildlife and support more than one million breeding seabirds and seals.
On an initial October trip, researchers observed an unusual amount of deaths in seal pups before conducting further surveys in January.
The confirmation of deaths doesn't immediately change the risk to mainland Australia, scientists from the Australian Antarctic Program say.
The federal government says it is preparing for a potential outbreak in Australia, noting the strain would have significant impacts on wildlife and the agriculture industry.
It has invested a total of $113 million to strengthen preparedness.
"For now we're free from the serious and contagious H5 bird flu," Minister for the Environment and Water Murray Watt said.
"But as it continues to spread globally, we must be realistic about the likelihood of an incursion here."
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