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 virus.
"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."
While wild birds will be vaccinated if possible, the priority will be on birds in captivity.
The federal government says it has secured 1500 vials of the vaccine, worth about $2 million.
"The doses vary depending in those vials of the size of the bird," Ms Collins said.
"We have sufficient vaccines in terms of undertaking the initial vaccination program, but we've also been very clear we're working with states and territories, and if we need more vaccines, we're able to secure those."
Australia's Chief Veterinary Officer Beth Cookson said vaccines would not be the silver bullet to stop the spread of the bird flu.
"It is not a standalone solution. Biosecurity will remain important, the protection of these species," she said.
"We have been working very carefully for the last 18 months as part of our national preparedness to make sure that we have safety and efficacy data available to us."
More than 200 bird flu deaths have been reported, with the majority of cases in South Australia.
While the flu was first detected in migratory birds, it soon spread to native species.
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.
Influenza vaccination expert, Adelaide University associate professor Mohammed Alsharifi, said the rollout of the immunisation would be crucial.
"It's the right approach if we want to keep or conserve those species, because the virus is very lethal and we've seen dead animals around in the news everywhere," he said.
"We need to remember the virus may mutate. But at least if we have good immunity against the clade (variety) of the virus that's circulating, then it will be the right approach."
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