The minister said the Government had also invested $2.13m in 31 other pest control initiatives announced last week.
She said the funding announced today came on top of $11.2m set aside for kiwi recovery on this year's budget.
Friends of Flora would receive $103,863 to translocate up to 12 great spotted kiwi into the Flora project area in Kahurangi National Park. It was hoped this project would increase genetic diversity in the local kiwi population.
$83,616 would go to Te Runanga o Te Rarawa for the Warawara Restoration project in Northland. This project aimed to develop a new kiwi "aversion training programme" for dogs, development of a dog control strategy and community advocacy
The third group to get funding, Thames Coast Kiwi Care, would receive $39,000 to oversee stoat trapping, predator control and monitoring of the Coromandel brown kiwi population in the Te Mata Valley.
The Government has gone ahead with boosting funding for some kiwi projects despite contrary advice from the Treasury.
In July, it was revealed the Treasury said a project to protect the country's national bird was "not aligned with overall Government priorities".
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 the Budget 2015 information release.
The Greens have previosuly accused the Government of using the Save Our Iconic Kiwi project to distract people from a broader set of of cuts to conservation funding.
The Greens said DoC's natural heritage management programme had its funding slashed from $166 m to $159m.