Department of Conservation (DOC) Mahaanui operations manager Andy Thompson said efforts were made to refloat the whale but it had been out of the water for some time and was beginning to suffer.
The decision to euthanise it was made in consultation with iwi, based on the animal's welfare.
The stranded whale was reported to DOC early Wednesday morning.
An aircraft was sent out to fly over Kaitorete Spit and Banks Peninsula to see if the pod remained in the area - but none were seen.
Thompson said the chance of successfully re-floating a pilot whale without its pod is low.
Pilot whale strandings on Kaitorete were not common, but the Banks Peninsula area was a hotspot for a wide range of marine life, and it was not unusual for pilot whales to be in the area, Thompson said.
A Project Jonah medic and Christchurch City Council staff were also on site.
In an earlier social media post, Project Jonah said: "Teams are assessing the welfare of the whale, large waves and conditions to see if refloat is to be attempted."
The whale will be buried on the spit.
