Authorities said the 10-month-old bearded collie crossdog, called Grizz, could not be captured after it ran off.
The dog was training to be an Aviation Security explosion detector when he escaped handlers who spent hours trying to coax him away from the runway. Grizz was just six months from graduation.
The incident grounded 16 flights and caused delays for several hours.
An airport official said the decision to shoot the dog, handled by the government's Aviation Security Service (Avsec), was a last resort.
"We tried everything, food, toys, other dogs, but nothing would work ... In these difficult circumstances the Airport's Emergency Operations Center team decided to have the dog destroyed," Avsec spokesman Mike Richards said.
But it has been met with outrage, with many asking why the dog could not have been tranquilised instead.
SAFE for Animals Ambassador Hans Kriek condemned the killing, asking why the animal wasn't tranquilised, but the CAA spokesman said he "didn't believe" that had been an option.
Auckland Airport originally announced on their official Twitter they had captured the dog, before revealing an hour later that he had been killed.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)