The deaths came after 19 of the birds were moved by New Zealand department of conservation officials last week to an isolated island, where it is believed they were killed by bacteria not present in their original home.
Recovery programme leader Paul Jensen said because vaccination had been successful with turkeys they would use it on kakapo, of which there are only 83 left worldwide.
The conservation department said workers on Chalky Island, at the bottom of New Zealand's South Island, were rounding up the total of 23 kakapo there so they can be isolated and the sick ones treated twice daily with antibiotics.
"We'll inoculate all the birds that are well, treat the ones that aren't and inoculate them as soon as they are well enough," he said.
Professor Maurice Alley, a veterinary pathologist at Massey University in Palmerston, said the bacteria, called erysipelothrix rhusiopathiae, was present in the birds' new environment but not Chalky Island, where they were taken from.
Conservation officials apparently did not realise the disease was on the island because older kakapo already established there had not fallen sick.
Older birds can carry the disease and spread it without showing clinical symptoms, and it can survive for up to 35 days in soil, but kill a susceptible juvenile bird within 24 hours.
Alley said the disease appeared to have mainly affected juveniles and caused acute septicaemia.
Pacific Vet Limited immunologist Kent Dietemeyer said they had sent a vaccine, normally used on pigs and farmed turkeys, to the conservation officials.
"It's all kind of new for them -- nobody has done any trials on these vaccines and kakapo so we'll just keep our fingers crossed," he said.
Kakapo (strigops habroptilus) is a nocturnal flightless bird that climbs trees. Adult males weigh up to 2.5 kilograms (5.5 pounds) making them the world's biggest parrots -- and with some living for around 100 years, they are among the longest-lived.
They have been under threat for a long time, being hunted by pre-European indigenous Maori. Europeans settlers later brought cats, ship rats, stoats, weasels, ferrets and possums, which found kakapo easy targets.
In the mid 1990s there were just 50 kakapo left, but an intensive breeding and feeding programme saw the numbers slowly increase.
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