As many as 140 pilot whales died after becoming stranded on Mason Bay on the west coast of the island.
The conservation authorities were alerted about the impending disaster at the weekend when a camper spotted the whales and hiked to the nearest field base to report what was happening.
According to DOC Rakiura Operations Manager Ren Leppens, half of the whales had already died by the time they were found. The remote location and lack of nearby personnel meant successfully refloating the whales was highly unlikely.
"However, it's always a heart-breaking decision to make".
Authorities said half the whales had already died by then, while the other half were put down as it would have been too hard to save them.
A 15-metre male sperm whale beached and died at Doubtful Sound on Saturday, while a female pygmy sperm whale washed up dead at Ohiwa over the weekend.
In a separate incident, 12 pygmy whales became stranded on 90 Mile Beach on New Zealand's North Island.
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Last year, 400 pilot whales were beached in Golden Bay, also in southern New Zealand, the third largest mass stranding in the country's history.
Several factors can cause strandings, such as the whales trying to escape predators, falling ill or navigating incorrectly. The two pods of pilot whales were beached about 1.2 miles apart from each other.
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.
The creatures can also beach if the tides dramatically change. However, the remaining had to be put down as it would have been hard to save them. They get their name from the way they travel in pods: One male leads the way as a "pilot" with the rest of the pod of up to 200 whales following.
While whale strandings are common in New Zealand - there are around 85 cases per year across the country - it is not known exactly why or how the whales end up in this situation.
DOC has notified local iwi Ngāi Tahu and is working together on next steps. Two have since died, with efforts still underway to "re-float" the remaining creatures.