"Any refloat attempt would have meant having people more than one kilometre out to sea in chest-high water and that is a safety concern," said Greg Napp from the Department of Conservation.

Forty-nine long-finned pilot whales were stranded on Sunday in a remote area of the country's South Island known as Farewell Spit. Eight died soon after beaching in a shallow tidal area and the remaining 41 were shot.

"Given the hopelessness of being able to successfully refloat the whales, our prime concern was then to avoid the whales suffering a long and painful death," Napp said.

"The whales were one kilometre out from shore and spread over six hectares," Napp said.

The whales were not thought to be from the same pod of more than 100 whales that stranded in the same area two weeks ago. That group was able to be re-floated.