DoC was forced to end the misery of seven mammals that re-beached themselves.
The most ambitious whale rescue attempted in New Zealand was being hailed a success last night after 14 of the mammals were refloated.
About 7.30pm, rescuers' tense expressions were replaced by whoops of delight as 21 pilot whales were refloated at Rarawa Bay in the Far North, 50km south of where they and about 50 others got into trouble at Spirits Bay on Wednesday.
But over the next hour, seven re-stranded themselves, and Department of Conservation incident controller Jonathan Maxwell said there was no option but to euthanise them.
"By that stage it was dark, and all of us were pretty exhausted. We all agreed we had done everything we could for these animals. The most humane course of action was to end their suffering," Mr Maxwell said.
Despite their loss, DoC operations manager Patrick Whaley said the rescuers were elated, knowing 14 whales had been saved.
Earlier, the exhausted, sunburned helpers had refloated the whales as the wind began picking up - making their task difficult.
The mammals had been ferried to the beach in six trucks, packed in sand and hay and covered with wet cloth. The trip on winding gravel roads was too distressing for three, which died at Rarawa Bay.
Orca Research Trust founder Ingrid Visser said she was "devastated but elated" as the three-day toil neared its end. "I can't believe we lost three. They were within 30m of the sea, so close," she said tearfully.
"The trip was too much for them. But if we didn't try we would have lost them all."
For the refloating, three larger whales were pontooned about 700m offshore, while the others were corralled together, then released en masse, said DoC community relations manager Carolyn Smith.
"DoC staff and volunteers working with three boats and two jetskis attempted to herd all the whales back out to sea. However, over the course of the next hour, seven re-stranded."
Mr Whaley said DoC had transported whales by road before, but never so many or so far.
He said it had been crucial to complete the move yesterday. After three days of little sleep and rough weather, the volunteers had started to burn out. Some had not rested since Wednesday night.
Yesterday, they had reinforcements from as far away as Wellington. Anti-whaling campaigner Pete Bethune drove from Whangaparaoa to help. He joked that the rescue was "a little more low key" than his recent adventures with the Sea Shepherd conservation group, which led to his being jailed in Tokyo. "But it breaks my heart to see whales flapping helplessly ... and when it comes to help, the more the merrier."
The refloating marked the end of an arduous project involving more than 120 helpers from DoC, Ngati Kuri, Project Jonah and Far North Whale Rescue.
DoC contractor Nellie Norman first spotted the pod struggling in the rugged surf on Wednesday.
She said she could not believe the project she had sparked. "Three days ago I saw them while working alone and now we have a hundred people, diggers, trucks and a community who have come to this faraway place ... I didn't expect this."
* Wednesday: At least 70 pilot whales struggle in surf or become stranded at Spirits Bay. Helpers battle to keep two dozen alive.
* Thursday: The whales are moved to a river near Spirits Bay.
* Yesterday: The survivors are driven to Rarawa Bay. Three die, 21 are refloated. Seven later re-beach.
- Additional information provided by Department of Conservation