Instead, resources should go into saving species that have more chance of recovering and surviving in the evolving environment.
"It's a wonderfully weird creature and it's a shame that we will probably lose it regardless of any interventions. Harsh, but somebody's got to say it," said Cory Bradshaw, of the University of Adelaide's director of ecological modelling.
Using a mathematical formula, Professor Bradshaw and colleagues from Adelaide and James Cook University, in northern Queensland, created a new index called Safe (Species' Ability to Forestall Extinction), which ranks the probability of animals becoming extinct based on population.
The index goes a step further than the Red List of Threatened Species, produced by the International Union for Conservation of Nature, which ranks animals and plants in categories from safe to critically endangered.
"It really comes down to accounting, are we deliberately or inadvertently losing hundreds if not thousands of species by putting money into species that are a lost cause? That doesn't mean we go out and knock every one on its head though," Professor Bradshaw said.
Other endangered animals that could be left to die off because of unsustainable population levels, according to the index, include Australian's hairy-nosed wombat and the Javan rhinoceros.
The Conservation Department said it would look at the merits of the index but said it would continue to support the Kakapo Recovery Programme.
"DOC is very proud of the work that's been done to save the kakapo and we've no intention of letting them go," spokesman Chris Pitt said.
Kakapo have taken decades to save from "dangling on the cliff of extinction", Forest & Bird conservation advocate Nicola Vallance said.
The programme, based on several small islands, has rejuvenated the number of kakapo from 50 in 1995 to 120.
"I think any New Zealander would say they're absolutely worth protecting," Ms Vallance said.
DOC spent nearly $39 million on threatened species programmes in the year ending June 30, 2010.
Twenty native birds are extinct and 77 are threatened – made up of 24 critical, 15 endangered and 38 vulnerable birds.
Professor Bradshaw, who encountered kakapo while studying at Otago University, said any animal with a population below 5000 had a greater risk of extinction because they could be wiped out by extreme events such as cyclones or forest fires.
He admitted the concept was unpopular but the index would assist "conservation triage" – prioritising the species that should be saved.
Massey University's Doug Armstrong, who specialises in conservation biology, said there had to be a "trade-off" when picking what animals to save but it was not up to scientists to make this decision.
It was up to New Zealanders and, in some circumstances, iwi, which had a special connection to certain species, to weigh up the benefits, cost and value of saving an endangered animal.
"I would be very hesitant to write off species just because they have low numbers," Professor Armstrong said.