The 8-week-old puppies, one male and one female, were otherwise in a good, healthy and clean condition, the SPCA said.
Ms Kalin did not want to speculate on whether the puppies had been stolen or whether their owners believed they could no longer care for them, as an investigation was underway.
But she did advise pet owners in the area to keep their animals in their homes at night.
Ms Kalin said the organisation would "hold accountable" anybody found to have inflicted cruelty on animals.
"The reason why we should take these matters seriously is not only from an animal welfare perspective but also from a community perspective, because there's now evidence linking animal cruelty and violence towards people," Ms Kalin said.
The SPCA has going door to door to try to find the owners of the pups.
Their bodies have now been sent to a veterinary pathologist to determine the cause of death.
The SPCA posted information about the incident on its Facebook page in a bid to garner more information from the public. The post, which described the discovery as "horrifying", has been shared by almost 1000 people and has more than 100 comments.
One person said she came across a dead cat in Belmont last week and wondered whether the two incidents could be related
Another woman, Caroline Davison, said: "I detest people who do these things to defenceless animals - cowardly, hurting something so defenceless."
Emma Dean said: "Hope they find these people, if they can do that to animals they can do it to children, look forward to the news of them being found!"
Anyone with information about the incident was asked to contact Senior Inspector Kevin Plowright on 09 256 7300.
