Hikers on Sunday reported finding 107 whales beached on Stewart Island, off the South Island`s southwest coast, a Department of Conservation (DoC) spokesman said.
He said some of the whales were already dead and DOC rangers had to euthanise the 48 remaining survivors as there was no prospect of refloating them.
"We were quickly aware that it would be at least 10 to 12 hours before we could attempt to refloat them and that given the hot, dry conditions many more would soon perish," he said.
The spokesman said a storm was also bearing down on the beach near Mason Bay where the whales were stranded, making it too dangerous to try to get them back into the sea.
"We were worried we would be endangering the lives of staff and volunteers," he said.
Pilot whales up to six metres (20 feet) long are the most common species of whale seen in New Zealand waters.
Mass strandings are common on the country`s rugged coast. Earlier this month, 14 died after beaching near the South Island tourist city of Nelson and 24 perished last month near Cape Reinga in the country`s far north.
Scientists are unsure why pilot whales beach themselves, although they speculate it may occur when their sonar becomes scrambled in shallow water or when a sick member of the pod heads for shore and others follow. (C003/K004)