A brown skua and a northern giant petrel had tested positive for the H5N1 strain of the flu after they were found in Western Australia, federal Agriculture Minister Julie Collins confirmed on Monday.
There has been no evidence of mass mortalities among birds, with both animals discovered on a remote beach in Esperance, about 700km southeast of Perth.
"We are working to determine whether or not the H5 bird flu has established in the wildlife or established in Australia, other than these two isolated birds," Ms Collins told reporters.
The poultry and agricultural sectors are free from the flu, with samples of the infected birds to be investigated over the next week.
It was too soon to call whether the confirmed cases would have an impact on egg or chicken prices, Ms Collins said.
"We have done all the preparedness and all the work and we have learnt from (previous) infections and overseas from keeping it out of the agricultural production,'' she said.
"Can we do that forever? We don't know ... we are certainly working very closely with both the chicken meat and the egg poultry system and industries to do everything we can do and improve biosecurity in those systems."
A hotline for members of the public to report their concerns has been established, as more than a dozen cases of sick or dead birds are reported.
Despite there being no detections in commercial poultry, major chicken producer Inghams Group announced it would mitigate against any potential risks across all WA sites.
"This includes the implementation of a complete lockdown, preventing all non-essential access, across all the company's WA farms and processing operations," the company said.
The meat producer is seeking a regional housing order from the state government that would allow free-range poultry to be kept indoors.
Australia had been preparing for the deadly avian flu for years, as the only continent previously unaffected by the strain, chief veterinary officer Beth Cookson said.
"Our actions at the moment are really to understand whether these two single individual birds have been able to spread it into other populations in Australia," Dr Cookson told ABC Radio.
"Our approach is to really learn from the overseas experience and look at the practical actions that can be put in place to mitigate the impacts as far as possible."
She said the two sick birds had a breeding habitat on the sub-Antarctic territories Heard Island and McDonald Islands, where the strain has killed 13,359 southern elephant seal pups.
People are urged to report any sick or injured bird they come across, but to keep their distance as the virus can spread to humans in close proximity omn rare occasions.
The federal government has developed more than 100 response plans for key sites and vulnerable species and invested about $100 million in preparedness.
The discovery has fuelled fears among scientists, conservationists and agricultural groups, who point to mass deaths and species-level population reductions overseas.
University of Melbourne researcher Michelle Wille said international experiences painted a gloomy picture.
"Everywhere this virus has emerged has been really catastrophic, with mass mortality events in wildlife, and in some places, we've seen species-level reductions in population," she said.
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