The incident comes days after around 145 pilot whales were stranded and died on a remote beach on Stewart Island.
Five of the six remaining pygmy whales have beached again in Northalnd and DOC experts have made the decision to euthanise them.
Overnight, the creatures were safeguarded in a shallow stream to relieve the pressures on their bodies as the countdown began to re-float them offshore.
None of the 28 whales stranded on a beach in Australia's Victoria state are expected to survive, in the latest major beaching amid the animals' annual migration in the Southern Hemisphere, said environmental authorities on Wednesday.
But he said the whales became too buoyant and were moved onto the sand, where volunteers kept a vigil through the night, regularly cooling the animals with water.
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Mr Turner said the whales would probably be euthanised if their condition had not improved.
The shooting of the remaining whales was prompted by the remote situation of the island as well as the lack of adequate personel as well as the deteriorating heaslth of the whales. "It was useless - they were so big and heavy and the realization we could do nothing to save them was the worst feeling I've ever experienced".
"There could be sharks in the area as well, it's probably a great spot to stay away from", Turner told 3AW on Wednesday morning.
Half the animals were already dead and the rest were put down because there was no chance of rescuing them from the remote location USA travel blogger Liz Carlson was among a group of hikers on Stewart Island that found the whales and she described her frustration at being unable to help the huge sea creatures.
According to the DOC, marine mammal strandings are common on New Zealand shores, with the DOC responding to an average of 85 stranding incidents each year. "More than one factor may contribute to a stranding".