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The organisation told the Herald it was investigating the "cruel act" and police had been alerted.
Animal rescue charity Paw Justice has now offered a $1000 reward for information that leads to the prosecution and conviction of whoever was responsible.
"We want justice for these puppies," co-founder Craig Dunn said.
The bag had been found in an area known as "The Elbow", on the banks of the Waikato River south of Waiuku about 2pm Friday.
The puppies were black with white paws and found in a black bag with a silver fern and "New Zealand" written on it.
"This act was absolutely disgusting," Dunn said. "We know with Covid-19 and the economic impact there are a lot of added stresses, and we feared, in the same way domestic incidents have increased, animal abuse would also.
"Whoever has done this needs to be brought to justice. It shows a complete lack of empathy."
The puppies were taken to the SPCA centre in Māngere, where they were assessed by a vet.
SPCA northern region general manager Jen Radich said they had contacted police while also launching their own investigation.
"There are always people and organisations who can help and resorting to this kind of cruel act is absolutely unnecessary.
"It appears that these puppies have been intentionally drowned, which means they mostly likely would have suffered.
"We take these types of incidents very seriously and it's an active investigation."
The puppies were not newborn, but were at least 15 weeks old.
"Someone must know something," Radich said.
"If anyone has any information on who may be responsible, please call SPCA."
Radich said help was always available for pet owners for low-cost desexing.
"Unwanted animals are most often the result of an animal that has not been desexed and continues to have litter after litter, so we urge people to contact SPCA or their local vet to book an appointment.
"It's a simple fix and goes a long way towards responsible pet ownership.
"Help is always available for low-cost desexing, please contact your SPCA."
Anybody with information could contact Paw Justice at info@pawjustice.co.nz, with the title "REWARD".