Wildlife officials remain hopeful a world-first vaccination program can protect Victoria’s little penguins, despite fears the deadly bird flu response has come too late.

A program to vaccinate more than 5,000 little penguins across Phillip Island and St Kilda will begin on Monday night.

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Each bird will need to receive two doses of the H5 bird flu vaccine and will be microchipped.

The unprecedented rollout follows the death of an infected little penguin on Phillip Island, the first confirmed case involving the species in Australia.

The discovery has fuelled concerns the vaccination effort may have come too late to prevent the virus from spreading through the colony, placing more penguins at risk.

Victoria’s Chief Biodiversity Officer James Todd told Sunrise on Monday that while authorities were “hopeful” the vaccine will work, it would not fully stop H5 bird flu from circulating and could not guarantee the penguins would avoid infection.

“We are hopeful that the vaccine can work; of course, this is still uncharted territory, and there are still lots of complexities and risks involved,” Todd said.

Victoria’s Chief Biodiversity Officer James Todd said authorities remain hopeful the bird flu vaccine roll-out will work. Credit: Sunrise

The vaccine has already been trialled on little penguins and several other species, with the vaccinated animals developing an immune response.

“Observations have also indicated no impacts on health of those vaccinated animals,” Todd said.

Todd said now was the “perfect time” to begin vaccinating the colony, with relatively few birds currently returning to their nests.

“At this time of year, most birds are out at sea still feeding, so there’s only a few hundred returning to the nests at this time of year, we’ll start to see that increase over the coming month,” he said.

The rollout faces significant logistical challenges because every penguin must be caught twice to receive both doses.

“One of the challenges of vaccinating live animals is that there needs to be two doses of the vaccine administered. That’s almost impractical and impossible in most wild populations.

“In the case of little penguins both at Phillip Island and at St Kilda, the penguin parade colony is very well-known, their nesting habits are well known, they’re very used to dealing with humans and under the spotlight at night-time, so it makes them a candidate case,” he said.

“But of course, this is not without complexity and challenges,” he said.

The program is believed to be the first of its kind anywhere in the world involving an H5 vaccine being administered across a wild bird population on such a scale.

Members of the public have been urged not to touch sick or dead birds and to keep pets away from wildlife and carcasses.