CSIRO testing confirmed the deadly strain in a greater crested tern found at Robe, federal Agriculture Minister Julie Collins said.
It is the first time H5 has been detected in a native Australian seabird rather than a migratory visitor.
"While this is a concerning development, it is not unexpected and is another sign that our strong biosecurity system is working," Ms Collins said.
Two fresh cases in SA and one in Western Australia have also been confirmed as H5, bringing the total number of detections to 12.
Another suspected positive in WA is undergoing testing.
There is still no evidence of mass deaths in wildlife, no infections in commercial poultry or other agricultural animals and the risk to human health remains low, authorities say.
The SA government is leading an enhanced surveillance operation around Robe, about 340km southeast of Adelaide, to check for any further spread, while federal experts — including Australia's Chief Veterinary Officer — continue to monitor the situation.
Officials are urging people not to touch sick or dead birds or wildlife, to keep pets away, and to report unusual bird deaths or behaviour to the Emergency Animal Disease Hotline on 1800 675 888.
More information is available at birdflu.gov.au and pir.sa.gov.au/birdflu.
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