"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.
The programme will increase pest control in 35 forests to protect 12 native species, and mainly involves using 1080.
Dr Smith said he was aware some people would object to the use of the controversial poison, but said it would not mean record use.
"Pre-feeding, improving bait quality to avoid crumbs attractive to birds, helicopter rather than fixed-wing aircraft distribution, GPS, and the development of repellents for non-target species have enabled major improvements in 1080 control methods," he said.
"Reason must trump prejudice about poisons when the very species that define our country, like kiwi, are at stake."
An additional 500,000 hectares will be treated this year, and will also see the expansion of DoC's pest control work by 50,000 hectares each year over 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.
The programme will cost about $21 million over the next five years, coming from DoC's $335 million annual budget, Dr Smith said.
The programme announcement was welcomed by Parliamentary Commissioner for the Environment Jan Wright, who described rats and stoats as "voracious predators" of native species.
"The potential toll on our native wildlife is enormous," she said.
"I am delighted with Dr Smith's considered response to this very major threat to New Zealand's native flora and fauna."
Dr Wright said the 1080 poison was "the only tool we have to control the plagues of rats and stoats that follow a mast".
She also said the logistical challenge of the programme should not be underestimated, and that the timing of drops was critical.
DoC director-general Lou Sanson said field staff would be closely watching the seed fall and rat-tracking results from key sites over the next few months.
"We need to be ready to act quickly to knock back rat or stoat numbers before they overwhelm birds which are particularly vulnerable during the spring nesting season.''
It was concerned that its existing trap and ground-based networks would be overwhelmed if predator numbers rose rapidly.
"Our best, and fastest, option for protection over large tracts of rugged bush is using biodegradable 1080 baits by air.''
Forest & Bird, New Zealand's largest conservation charity, backed an increase in the use of 1080 as a "fitting response'' and the level of its use over the next five years should become the new baseline if the ongoing battle against introduced predators is to be won. "Without this increase in predator control, there will be a real possibility that we will lose a bird species this mast year. Ground control operations carried out by Forest & Bird branches around the country are already reporting increased numbers of rats. That means the stoats will follow,'' Forest & Bird advocacy manager Kevin Hackwell said.
• Rats, stoats and possums kill an estimated 25 million native birds a year, or 2000 birds every hour.
• The beech tree mast this year is expected to bring an additional 30 million rats and tens of thousands of stoats.
• Two significant mast seasons in the last decade saw some bird species, like Mohua, wiped out entirely from some areas.
• The Battle for our Birds programme will inject $21 million into bird protection, targeting 35 forests to protect 12 native species.
• An additional 500,000 hectares will be treated with 1080 this year.
