All 61 pilot whales that beached themselves at the tip of Farewell Spit on Monday hjave died.
Two pods of whales became stranded on the spit at the top of the South Island - one group on Monday afternoon and a second overnight that night.
The Department of Conservation says the final 18 surviving whales were put down on Wednesday morning to end their suffering.
A DoC spokesperson John Mason says it had been hoped the whales would refloat themselves during high tides but they stranded again each time.
A rescue mission was ruled out because the whales were too far out from the beach.