They were taken to the SPCA centre in Māngere, where they were assessed by a vet.
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SPCA northern region general manager Jen Radich said they had contacted police while also launching their own investigation into the "cruel act".
"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."