Last month, the charity said it was "deeply concerned" over the use of 1080, and the use of poisons to kill animals due to the level of suffering they caused.
However, it seems it has now changed its stance, with a new statement saying it realised there was "a need for population control of some species".
"When it is justified, SPCA is not anti-pest control – but we advocate that when it is needed, it must be humane," it said.
The statement was released after the charity said it received lots of feedback and enquiries over the past month about the organisation's position on this topic.
Sodium fluoroacetate, more commonly known as 1080, is a poison, mixed into baits, and used to control the numbers of a range of mammalian species, particularly possums and rats.
The earlier release in January said the welfare of all animals should be viewed equally, and people should recognise that they deserve protection from suffering pain or distress, regardless of the species or where they came from. This included "so-called 'pest' animals".
The statement led to environmental organisation Forest & Bird calling the SPCA's position "naive", and one that would lead to "cruel deaths and extinctions" of native birds.
"Their position reflects their history of caring for domesticated animals such as cats and dogs, without understanding the needs of New Zealand's native animals and ecosystems," chief executive Kevin Hague said.
"While the idea of stoats and rats peacefully coexisting with native birds sounds great, the reality is that an estimated 25 million native birds, eggs and chicks are cruelly eaten alive by introduced predators every year in New Zealand."
In the new statement, the SPCA said all New Zealanders ultimately want the same outcome: a country where our native species are thriving.
"Our native species are our taonga and deserve our protection. We acknowledge that in some areas, particularly those where our native species and biodiversity are at risk, there is a need for population control of some species."
However, the charity said it still cannot support the use of poisons, and advocated that where pest control measures must be taken, they must be humane.
"SPCA would like to see New Zealand move away from a reliance on poisons, including 1080, with the ultimate goal of being able to stop their use.
"We are realistic and pragmatic and we understand humane alternative solutions take time to develop and implement," it said.
"But while we understand why poisons (such as 1080) are currently being used, as an animal welfare organisation we still can't support their use."
"We advocate for further research and development of humane alternatives to poisons as a matter of priority, and that they are implemented as soon as they are available."
To be able to move away from NZ's reliance on the use of poisons, the SPCA advocated for more investment into further research and development of humane alternatives to poisons.
Forest & Bird congratulated the SPCA for "listening to the experts", and "clarifying their position".
"This position is much more inline with the realities facing the folk on the ground working to save our forests and native animals," it said.