All 33 remaining stranded pilot whales have been euthanised after restranding again overnight in Golden Bay.
The whales were part of a pod of 99 that beached in the Farewell Spit area of Golden Bay around midday on Monday.
Volunteers have twice refloated surviving whales only to have them restrand, with more dying or having to be put down after each attempt.
Department of Conservation area manager John Mason said the remaining whales were shot in the head with a high calibre rifle shortly after the decision to put them down at 8:15am.
They were showing "significant" signs of physical deterioration and stress, with many bleeding and blistering in the morning sun.
He said gale warnings are forecast for this afternoon, meaning boats would not be able to accompany the whales even if they were refloated.
"It's a combination of all these things that's behind the decision. In the end they've had plenty of opportunities to go and they've chosen not to.
It's frustrating and it's very disappointing."
Mr Mason said a debrief would be held to see whether anything more could have been done to save the whales.
He was comfortable it was the right decision to put them down this morning.
"There are always people who say you should to more and you should be trying again - but you have to look at the bigger picture.
"We don't believe anything more could be achieved."
Project Jonah chief executive Kimberly Muncaster, who has been at Farewell Spit since Monday, said finding the 33 surviving whales restranded again this morning was extremely difficult for volunteers.
"This is tragic news. Unfortunately the stranded whales are now also further along the Spit and on the extreme boundary of our ability to reach them for another rescue attempt.
"Obviously the Project Jonah medics, DOC staff and other volunteers that have been working so hard on the Spit over the last three days are devastated by this outcome."
The decision to end the volunteer mission means 82 whales have died as a result of the mass stranding.
Seventeen whales were able to refloat at high tide on Monday night.
Ms Muncaster said volunteer efforts now had to turn to making sure those whales did not restrand elsewhere.
"We must now focus our efforts on the 17 whales that refloated themselves on Monday night, and make sure they remain safe."
She praised the efforts of medics who worked for three in difficult conditions and with little sleep.
"They gave everything they had."