Due to the remote area where the whales were found, half of them were already dead and others in critical conditions, others were in hardly accessible areas which made the authorities decide to kill them.
"Sadly, the likelihood of being able to successfully re-float the remaining whales was extremely low", said Ren Leppens, the Department of Conservation's operations manager on Stewart Island.
"However", he added, "it's always a heart-breaking decision to make".
The group said it planned to re-float the whales on Tuesday and has asked for volunteers to help.
Fearing that the dead whales would start swelling with gases as they began to decompose, the authorities sent in a team of workers in protective suits to start cutting holes in the carcasses.
Alarming as this incident may be, such strandings are not uncommon in New Zealand.
On Sunday, 10 pygmy killer whales were found stranded on Ninety Mile Beach, in the country's North Island.
Grover said there was usually at least one "significant" mass stranding a year. In fact, most strandings remain a mystery but wildlife experts say sickness, falling tide, extreme weather and being chased by a predator could contribute to beaching whales.
The 19km stretch of beach at Mason Bay could be "confusing" for whales, he said.
It remains unclear why, exactly, such mass strandings occur. In 1998 more than 300 whales beached themselves at the spot.
There are a number of factors that can cause whale strandings.
Since the beach is isolated, it's unclear how long the creatures had been stranded before they were discovered. Whales can only swim forwards and a tidal change can affect their sense of direction.
Only about 375 people live on Stewart Island, which is also called Rakiura.
How do whales get stranded?
DOC has notified local Ngāi Tahu iwi and is working together on next steps.
He said staff shot the whales and the carcasses would be left where they were for nature to take its course.
Beached whales were reported elsewhere around the country over the weekend but they aren't related to the massive sighting at Mason Bay.