A hiker discovered the beached whales stranded ashore Saturday on Stewart Island, a remote island with a population of about 375 people.
Rakiura operations manager Ren Leppens from the New Zealand Department of Conservation said the hard decision was made to euthanise the surviving whales. They chose to euthanize the remaining stranded whales because of the difficulty of accessing the remote location. He described the decision as "heart-breaking".
Conservation workers said they were left with no choice but to euthanise half of the whales as the chance of rehabilitating them was "extremely low".
The largest single stranding in recorded history happened in 1918 when around 1,000 pilot whales beached themselves on New Zealand's Chatham Islands.
A rescue operation is also underway on the north island's Ninety Mile Beach after ten pygmy killer whales were discovered on Sunday.
The DOC stated that they handle at least 85 incidents of strandings a year which are caused by sickness, navigational error or a chasing predator, amongst other reasons.
Leppens told The New York Times that the beach has had three previous mass strandings - in 1998, over 300 whales beached near Mason Bay. They euthanized the remaining whales, saying they couldn't be saved.
The tragic incident took place on Stewart Island - also known as Rakiura - to the south of New Zealand's South Island. Rescuers were unable to save two of them, but said they hope to re-float the remaining whales on Tuesday. More than one factor may contribute to a stranding.
The remote location of the stranding meant the whales that had not yet died had to be euthanised.
Whale strandings are relatively common in New Zealand during the Southern Hemisphere spring and summer.
DOC has notified local Ngāi Tahu and they are working together on what to do next.
Clean-up workers had to "pop" the bloated carcasses of up to 300 long-finned pilot whales that had died at a New Zealand tourist spot in February previous year to stop them exploding and becoming a health hazard. Two have since died and attempts were being made to re-float the rest.