Fourteen of the pod were unable to be saved and had died, Conservation Department spokeswoman Trish Grant said.
The whales came ashore at Golden Bay north of the city of Nelson on the tip of South Island on Friday afternoon.
About 100 rescuers had been unable to refloat the whales before darkness fell Friday night. The rescuers set up camp nearby with plans to try again at first light.
Grant said the rescuers returned to the site of the stranding Saturday morning to find the whales had gone. It appeared a high tide around midnight had allowed the stranded whales to free themselves.
"We don't know whether they have managed to swim safely out to sea or whether they may have stranded somewhere else along the coast," she said. "Some, even though they are refloated, do wash up dead later on because they've been through such an ordeal so they are considerably weakened by it."
Pilot whales are about 13 to 20 feet (four meters to six meters) long and are the most common species of whale in New Zealand waters.
Whale strandings are commonplace in New Zealand. Last month 24 pilot whales died after stranding on the North Island. In December 2009, more than 120 whales died in two separate beachings near Golden Bay and on the east coast of North Island.