The surviving pilot whales were euthanised after an assessment of the chances of a successful re-float.
About 145 whales who were stranded off New Zealand's Stewart Island are dead - with authorities forced euthanise about half of them.
The pilot whales were first spotted by a hiker on Saturday. Two pods of whales were found stranded two kilometres apart at the southern end of Mason Bay in Rakiura, Stewart Island.
Rakiura operations manager Ren Leppens from the New Zealand Department of Conservation said the difficult decision was made to euthanise the surviving whales.
"It's always a heartbreaking decision to make," he told New Zealand local media.
He said an assessment was made that there was an 'extremely low' chance of successfully re-floating the surviving whales.
"Sadly, the likelihood of being able to successfully re-float the remaining whales was extremely low. The remote location, lack of nearby personnel and the whales' deteriorating condition meant the most humane thing to do was to euthanise."
The Department of Conservation said it responds to an average of 85 marine mammal strandings a year.
It is not known precisely why whales and dolphin strand, but some contributing factors are thought to be navigational error, sickness, extreme weather, geography and in an attempt to escape from a predator.
Southland District councillor Bruce Ford said pilot strandings were not uncommon at Mason Bay.
"In days of old they would have harvested them [for whale oil]," he told New Zealand news site Stuff.co.nz.
Ten pygmy killer whales were also reported stranded at Ninety Mile Beach on New Zealand's North Island. Two have died, the remaining eight will be re-floated tomorrow.
Over the weekend, more whales lost their lives on New Zealand beaches, including a female pygmy sperm found on Ohiwa and a 15-metre male whale.