A hiker alerted authorities on Saturday night about the situation of the whales, who were stranded in Mason Bay in two separate groups about two kilometers apart, a Department of Conservation of New Zealand release said. By the time rescuers arrived at the scene, around half of the stranded pilot whales had already died.
Half of the whales were already dead and the rest were put down by conservation workers due to their condition.
Leppens said in a statement, "Sadly, the likelihood of being able to successfully re-float the remaining whales was extremely low". He described the decision as "heart-breaking".
The DOC said that it responds to an average of 85 stranding incidents a year, although most involve single marine mammals rather than entire pods.
All of the 145 pilot whales that stranded themselves on a remote New Zealand beach have died.
The rest of the whales were euthanised due to their deteriorating condition and the remote, hard access to the location.
Two died but there will be attempts to re-float the others as soon as they can be gathered more closely together, something that will increase their chances of survival.
The DOC said the two events were unlikely to be related.
A rescue operation is also underway on the north island's Ninety Mile Beach after ten pygmy killer whales were discovered on Sunday.
Stewart Island, also know as Rakiura, is home to around 380 people. "You wish you could understand the reasoning why the whales strand better, so you could intervene".
Since 1840, more than 5,000 strandings have been recorded around the New Zealand coastline.
The local Maori tribe, Ngai Tahu, is now working with DOC to bless the dead whales and make plans for burial of the remains.
There were a number of a reasons whale strandings occurred, including sickness, navigational error, geographical features, a rapidly falling tide, being chased by a predator, or extreme weather.
However, conservation officials note that these should not be confused with natural whale traps, such as the one at Farewell Spit, where whale strandings have been noted for centuries.