A group of experts will voyage to Heard and McDonald islands, 4000 kms southwest of Western Australia, as part of the nation's biggest campaign to the area in two decades.
Environment Minister Murray Watt, who joined the scientists in Hobart on Friday, said Australia was the only continent remaining free of the h5 strain of bird flu, despite it having spread globally.
"There are other Antarctic islands where we have seen bird flu and it's important for us to understand whether that may have occurred at Heard and McDonald islands as well," Senator Watt said.
Agriculture Minister Julie Collins said the 10-day mission would improve Australia's preparedness.
"We have ... as a government invested around $100 million in preparedness for the h5 bird flu ... to make sure that when bird flu does arrive, that we're as ready as we can be," Ms Collins said.
H5 avian influenza is a highly contagious strain that mainly affects birds, but can also infect other animals. It rarely affects humans.
Australian Antarctic Program head of division Emma Campbell said one of the main objectives of the voyage was to also assess the size and distribution of seabird and seal populations on the islands.
"This is really important for us to be able to get data that can feed into our threatened species recovery plans and also understand what's happening on these islands," Ms Campbell said.
Securing Antarctica's Environmental Future project lead Justine Shaw said Heard Island had some of the most warming glaciers in the world.
"I can see there's lagoons now where I once worked and did science 22 years ago," Dr Shaw said.
She said the expedition was expected to be "wet, wild and windy" but RSV Nuyina icebreaking ship was "cozy" and any biosecurity risks would be highly mitigated.
Another 25-day voyage will leave Hobart in November, focusing on marine and land science.
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