The first vaccines were set to roll out in coming days, Agriculture Minister Julie Collins announced on Tuesday.
Species in captivity will be prioritised for the vaccination based on their vulnerability and risk of catching the H5 strain of bird flu.
"We've been very clear that we cannot stop the H5 bird flu from spreading amongst wild birds, but we can take action to protect the species most at risk, and the vaccination is now part of that response," Ms Collins told reporters in Canberra.
"Australians should expect to see more spread and larger numbers, particularly of dead birds and mass mortalities around the country from the H5 bird flu, we have been very clear that this will continue to spread across the country."
More than 200 bird flu deaths have been reported, with the majority of cases in South Australia.
Ms Collins said reporting of the number of bird flu cases would also change due to the spread of the virus among species.
Counting the number of cases was no longer the most accurate picture of how the disease was spreading, the minister said.
"Our reporting will evolve to focus on confirmed H5 events and the developments that matter most, where the disease is spreading, new locations or species affected in emerging areas of risk," she said.
The deadly strain has not been detected in the poultry sector or in the broader agricultural industry to date.
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