A hiker discovered the animals strewn along the bay on Stewart Island late on Saturday.
About 75 were already dead and conversation workers later made the "heartbreaking" decision to euthanise the rest, which were in poor health.
"Sadly, the likelihood of being able to successfully refloat the remaining whales was extremely low," said Ren Leppens, the Department of Conservation’s operations manager for Stewart Island.
He added: “The remote location, lack of nearby personnel and the whales’ deteriorating condition meant the most humane thing to do was to euthanise.
"However, it's always a heartbreaking decision to make.”
The whales became stranded in two pods just over a mile apart at Mason’s Bay, about 22 miles from the island’s main settlement of Oban. Only about 375 people live on Stewart Island, also known as Rakiura.
Mr Leppens said many of the whales were partially buried in sand and were in a poor condition, indicating that they had been beached for at least a day before they were found.
Staff shot the whales and their carcasses have been left at the beach to let nature take its course.
"You feel for the animals, it's just a really sad event," Mr Leppens added. "It's the kind of thing you don't want to see. You wish you could understand the reasoning why the whales strand, so you could intervene."
Beached whales are relatively common in New Zealand during the southern hemisphere’s spring and summer.
The Department of Conservation said it responded about 85 strandings a year, although most involve lone animals rather than whole pods.
On Sunday, 10 pygmy killer whales were found stranded at Ninety Mile Beach on the west coast of the country’s North Island. Two have since died, but staff are to attempt to refloat the remaining eight.
A sperm whale also died after it was beached at Doubtless Bay, on North Island’s east coast, on Friday.
Strandings are believed to have a number of natural causes, such as escaping from predators, illness, navigation errors, and extreme weather. There is also growing evidence that military sonar can disorientate whales and dolphins and cause them to beach.
Beached whales often die of dehydration or because their organs are crushed under the weight of their own bodies.
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