Rescuers monitored the survivors as they swam away from Colville Beach on North Island's Coromandel peninsula, and by Monday morning they were reported well out to sea.
Department of Conservation workers and hundreds of volunteers helped re-float the 43 whales at high tide. The volunteers covered the stranded mammals in sheets and kept them wet through the day.
"Some 63 pilot whales stranded ... but it looks pretty good, we've got 43 live ones," Department of Conservation ranger Steve Bolten said as the pod swam out to sea.
Bolten said one of the whales may have been sick, or their sonar may have led them into the shallow harbor and they couldn't find their way out again.
Meanwhile on South Island, 105 long-finned pilot whales that stranded died Saturday, conservation officials said Monday.
Golden Bay biodiversity program manager Hans Stoffregen said they were discovered by a tourist plane pilot and only 30 were alive when conservation workers arrived.
"They were in bad shape. By the time we got there two-thirds of them had already died. We had to euthanize the rest," he said.
The whales had been out of the water for a long time.
"It has been quite hot and they were very distressed. You could see the pain and suffering in their eyes," he was quoted telling the Southland Times newspaper
Because the site is part of a nature reserve, the 105 whale carcasses were left to decompose where they stranded, Stoffregen said.
Large numbers of whales become stranded on New Zealand's beaches each summer as they pass by on their way to breeding grounds from Antarctic waters. Scientists so far have been unable to explain why whales become stranded.