As low tide approached early Sunday evening, around 300 pilot whales were heading out of Golden Bay in the northwest of the South Island and swimming towards the deep-water safety of Cook Strait.
The public has been warned about the dangers posed by "whales exploding" on Golden Beach, on the South Island, and the Department of Conservation (DOC) has cordoned off the area.
Department of Conservation spokesman Andrew Lamason said they were sure they were dealing with a separate pod because they had tagged all the refloated whales from the first group and none of the new group had tags.
Around 400 whales became beached at Farewell Spit on Thursday, with 300 of those sadly dying.
About three-quarters of the 400 whales that beached themselves on Farewell Spit on Thursday night died before rescuers arrived the next morning.
Pilot whales are not listed as endangered, but little is known about their population in New Zealand waters.
In recent days volunteers have formed human chains in the water to try to stop the creatures from beaching themselves again. Officials will soon have to start clearing the carcasses, Christophers said.
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"This morning we'll be getting people down there basically poking holes in them, letting the gas out of them", he told Radio New Zealand.
The saga appeared to be over on Sunday, after the last 17 surviving whales successfully returned to the ocean and rejoined a pod swimming just offshore.
The shallow, sweeping spit is believed to interfere with the whales' navigation systems and is a regular scene of mass strandings.
Volunteers at Farewell Spit worked to keep the stranded whales wet.
The agency is now trying to figure out what to do with the carcasses of the dead whales. In 1985, about 450 whales stranded in Auckland.
The bodies could take up to several months to decompose and turn into skeletons.
The DOC said they plan to move the dead whales with a digger further up Farewell Spit to the area of the nature reserve that is not open to the public.