According to pest control guidelines, Pindone was the bait of choice because it caused the least suffering, had a reduced danger to domestic pets and was a suitable means of controlling rabbits in the rugged areas found within the Manorburn reserve.
Pindone carrot was used in winter when food sources were most scarce and fewer young rabbits were present.
However, it posed a risk to humans and domestic animals.
Users of the reserve are unhappy with the council's decision to proceed and have launched a petition against it.
In October, public outcry against the use of the toxin at the reserve convinced the council to explore other methods of pest management; however, these methods were less effective, eradicating only 60 rabbits.
Lower Manorburn reserve working group member Nigel Murray visited the reserve with his dogs regularly and was concerned for people walking their pets, and other wildlife, if the council proceeded with the drop.
He understood the importance of managing rabbits at the reserve, but he believed not enough was known about the impact of Pindone on wildlife.
"I know rabbits are a problem that we need to get rid of, but we need to do it in a way so that we all enjoy [the reserve], that we're not killing the indigenous population."
Central Otago District Council parks and recreation manager Gordon Bailey said the method trialled last year was ineffective and Pindone was the most effective for the area.
"Pindone-laced carrot is the recommended initial control option with follow-up control of strategic night shooting to keep rabbits at MMS 3 or below.
"If council does not take control action now the rabbit population will rapidly increase even further through the spring as the breeding season kicks in.
"Council also needs to be a good neighbour as both the neighbouring farms to the reserve undertake significant feral rabbit control."