Wanaka Doc biodiversity ranger Flo Gaud said rabbits attracted predators to the island, resulting in three buff weka deaths in one week in February this year.
The alleged culprits - a ferret and a stoat - were trapped and killed.
The island's remaining three buff weka residents were recently relocated to the predator-free Mou Waho Island so the poisoning operation can begin.
If rabbits were eradicated it should remove a main reason for stoats and ferrets to go to the island.
"While the predators swim to the island to feed on the rabbit population, the weka proves to be an easier prey," Ms Gaud said.
Rabbits have also caused major damage to native vegetation, further damaging the weka habitat.
The department will use a helicopter to distribute cereal baits containing the pesticide Pindone, which will be trickle-fed using a specially designed bucket supported by GPS technology.
The patch poison operation will target high-density rabbit sites.
Buff weka would be reintroduced to the island once it was declared safe from poison residue.
The island was inhabited only by breeding pairs and has been the nucleus of the Buff Weka Translocation Project, a joint Ngai Tahu and Doc project in which 400 birds have been introduced to islands in Lakes Wanaka and Wakatipu.
Te Peka Karara is one of eight sites around Wanaka that will be targeted for rabbit control during July.
Signs will be in place for the next eight months, until all toxic residue in carcasses has disappeared. More information is at Doc's Wanaka office.
Anyone visiting the island or other control sites should avoid touching baits. Children and dogs should be supervised at all times. Dogs are particularly susceptible to poisoning from baits and carcasses.
