The Treasury shot down a bid to save kiwis, saying a project to protect the country's national symbol was "not aligned with overall Government priorities".
The Government went ahead anyway, boosting funding for the "Save Our Iconic Kiwi" project in this year's budget.
Although Treasury supported several other conservation projects, it said the project "to reverse decline and secure an increase in kiwi numbers and distribution" was a dud.
The comments about the Department of Conservation (DoC) initiative were made in a paper dumped in today's Budget 2015 information release.
Last month, a report from the Local Government and Environment Committee said there were fewer than 70,000 kiwi left in the wild, with the population declining by 2 per cent a year due to predation.
Minister of Conservation Maggie Barry told the parliamentary committee the $11.2m project would focus on growing the kiwi population to a sustainable level through careful monitoring programmes and predator extermination.
DoC-funded kiwi sanctuaries would be set up so kiwis could be released into safe, predator-free environments.
The Greens accused the Government of using Save Our Iconic Kiwi to distract people from a broader agenda of cuts to conservation funding.
"The much-vaunted $11.2 million directed to the grandly titled 'Save Our Iconic Kiwi Initiative' is funded from DoC's natural heritage management programme, which has been cut from $166 million budgeted in 2014/15 to $159 million," Green Party MP Eugenie Sage said after the budget announcement.
"There is no genuine commitment to saving our national symbol when the Government is cutting funding for DoC's wider programme of maintaining, restoring and protecting habitats and species and simply ring fencing some money for kiwi work," she added.