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Two groups of pilot whales were discovered a little over one kilometer away from Mason Bay on Stewart Island, a sparsely populated island in the south of the country.
The authorities were first alerted by a hiker on Saturday night. Half of the whales were already dead. The remaining animals were then euthanized, according to the New Zealand Department of Conservation (DOC).
Ren Leppens, Director of Stewart Island Operations for the DOC, said that the remoteness and condition of the surviving whales made it impossible to save them. He called the decision "heartbreaking".
The DOC also announced that he was working with a local Maori tribe on "next steps". In New Zealand, Maori groups often participate in the dismantling and burial of whale remains stranded in accordance with indigenous traditions.
The incident is part of a series of recent strandings of whales in New Zealand. On Sunday, 10 pygmy killer whales were found stranded on Ninety Mile Beach, on the northern island of the country. Two have since died, while efforts are still underway to "revive" the remaining creatures.
The DOC has indicated that it meets an average of 85 stranding incidents a year, although most involve isolated marine mammals rather than whole pods.
The exact reasons why whales and dolphins have gone aground are not fully understood. Contributing factors may include "disease, navigational error, geographical features, a rapidly falling tide, being pursued by a predator or extreme weather conditions," the DOC statement said.
The largest would have occurred in 1918 when approximately 1,000 whales stranded on the Chatham Islands.