Scientists in October raised the alarm after observing an unusual amount of dead southern elephant seals on Heard Island, more than 4000km southwest of Perth.
The Southern Ocean island is part of Australia's external territory. Australia is the only continent yet to be affected by the H5 strain.
The federal government on Tuesday said testing of samples collected from Heard Island confirmed the presence of the strain in southern elephant seals.
The results were not unexpected, given the virus exists at the nearby French Kerguelen and Crozet sub-Antarctic islands, the government said.
"This detection of H5 bird flu on Heard Island does not substantially increase risks to Australia," Agriculture, Fisheries and Forestry Minister Julie Collins said.
"(However) it does reinforce the ongoing need for Australia to remain focused on preparing for a potential outbreak."
Australia's status of being free of the H5 strain remained unchanged, the government said.
There have been no observations of unusual deaths in other species on Heard Island, including penguins and other seabirds.
A second research voyage to the island, scheduled to get there in late December and return to Hobart in February, will gather further information about wildlife health.
The government and experts have said the strain's arrival in Australia is an inevitability.
An outbreak would have significant impacts on wildlife and the agriculture industry, especially poultry, the government says.
The Invasive Species Council has warned greater surveillance and more boots on the ground are needed to prepare for its arrival.
The government has invested more than $100 million to strengthen bird flu preparedness and enhance Australia's response, including the delivery of rapid-response equipment.
Researchers were monitoring the global spread of bird flu so Australia was equipped with the best information for when the virus reaches our shores, Environment Minister Murray Watt said.
The World Heritage-listed Heard Island is home to a vast array of wildlife and is an important breeding ground for various penguin species.
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