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Rat and stoat numbers are expected to skyrocket this year as their food supply is boosted by an unusually large seed drop from beech trees, known as a mast.
The boom in predator numbers threatens to put immense pressure on the country's already-endangered native birds.
Doc's five-year battle plan will double the amount of conservation land protected through the use of 1080.
Forest & Bird welcomed the plan, but believed the $21 million cost of the project should not come out of Doc's already-stretched budget.
"This is a situation that occurs very infrequently," advocacy manager Kevin Hackwell told Radio New Zealand today.
"It's an exceptional situation, particularly where you're talking about it happening potentially over the whole of the South Island, in which case we don't think it should be something that comes out of base funding for the Department of Conservation, and particularly out of the savings they made last year by getting rid of so many staff.
This is something the Government should be able to step up for and actually provide the extra resources."
Kevin O'Connor, Doc's acting director general, conceded that money would need to be shifted from other areas to boost the eradication effort.
"We're confident we can still deliver on everything else we're wanting to deliver on. We're able to, in some cases, defer some work and in other cases reduce the programme a little bit in order to do this higher-priority work.
"So it's just about setting priorities, and this is a very high priority for us."
Mr O'Connor told Morning Report that despite the reduction in staff numbers, Doc was confident it had the experience it needed to succeed.
"The loss of experience is always a problem of course."
Conservation Minister Nick Smith said Doc had an annual budget of $335m, which was stable for the next five years, and it needed to juggle its funding year to year.
He said the department has been spending a huge amount of money trying to find alternatives to 1080, when "we have now come to the conclusion, actually, for the foreseeable future 1080 is the best tool that we are going to have to be able to deal with the 25 million birds a year that are killed by pests."
Speaking to the Rotary Club of Nelson last night, Dr Smith said programme would increase pest control in 35 forests to protect 12 native species, and mainly involved using 1080.
The country's native birds were in decline, and the kiwi would not exist in the wild for our grandchildren unless we did more to protect them, he said.
The problem was "particularly urgent" this year, because the country was facing a one in 10-15 year large beech mast, which was expected to drop around a million tonnes of seed this autumn.
"This flood of food will trigger a plague of an additional 30 million rats and tens of thousands of stoats. When the seeds germinate in spring, these starved predators will annihilate populations of our endangered birds," he said.
An additional 500,000 hectares wold be treated this year, and Doc's pest control work would expand by 50,000 hectares each year for the next five years.
The plan is aimed at helping to protect the great spotted, brown and tokoeka kiwi, kaka, kea, whio (blue duck), mohua (yellowhead), kakaraki (orange-fronted parakeet), rock wren, long and short tailed bats, and giant snails. But is expected to also help save other native birds, reptiles, insects and trees and plants.
- Rats, stoats and possums kill an estimated 25 million native birds a year, or 2000 birds every hour.
- Two significant mast seasons in the last decade saw some bird species, like Mohua, wiped out entirely from some areas.
- additional reporting by Patrice Dougan