A hiker reportedly spotted the whales on Saturday and notified Department of Conservation staff at 10.30pm.
Ren Leppens, Rakiura operations manager at the Department of Conservation, said it had been a "heart-breaking decision to make". They chose to euthanize the remaining stranded whales because of the difficulty of accessing the remote location.
In the far north of New Zealand, eight pygmy killer whales were transported by truck to the east coast from the west where sea conditions were too rough to refloat them.
Stranded marine mammals are a common occurrence in New Zealand with the DoC responding to about 85 incidents a year.
The DOC did not say what had caused the stranding, but added that sickness, predators or extreme weather could have been factors.
Because of the isolated nature of the beach that the whales washed up on, it is thought that they were stranded for more than a day before they were eventually discovered late on Saturday evening.More news: Manchester United's Victor Lindelof (thigh) expected to miss a month
The rest were in very bad health and were euthanised, due to the lack of potential rescuers and the difficulty they would have faced in reaching the location.
Alarming as this incident may be, such strandings are not uncommon in New Zealand.
The DOC also announced that it was working with a local Maori tribe on the "next steps". A mass sighting like this is rare, the DOC said.
The best way to discover the cause of the stranding would be to conduct an autopsy on the whales that had stranded first, although that would be hard to determine now.
In 2017, more than 650 pilot whales beached themselves along Farewell Spit at top of South Island in two separate mass strandings.
Although there are many theories as to why whale beachings occur, no one has been able to find a definitive answer. One of the strandings involved more than 400 pilot whales, making it the largest of its kind in New Zealand for nearly a century.
Two have died since they were found on Sunday, but hope remains for the other ten creatures.