The H5 strain of bird flu was first detected on Heard Island in the Southern Ocean late last year, when researchers said hundreds of southern elephant seal pups had been found dead.
Heard Island and McDonald Islands, located 4,000 kilometres south-west of mainland Australia, are a haven for breeding seals and seabirds in the Southern Ocean.
The researchers estimate 13,359 seal pups succumbed to the disease out of a total population of 17,364 — more than three-quarters of the cohort on Heard Island.
But they say the figure could be even worse because the mortality was ongoing when they completed their observations, and some seal harems were losing up to 97 per cent of pups.
If the virus spreads to other parts of the sub-Antarctic, as well as Australia, they say it could have "potentially catastrophic" impacts.