Another 200 whales were stranded on a New Zealand coastline late Saturday, frustrating rescuers who had battled through the day and even defied a shark threat to try and keep them at sea.

At twilight, Department of Conservation (DOC) officials made the decision to leave the whales overnight as it became too risky to continue efforts to refloat them as darkness approached.

The crisis began Friday when a pod of 416 whales became stranded on Farewell Spit in Golden Bay on the northwest of the South Island.

Most of them died but volunteers converged Saturday on the spit, which is a notorious whale trap, to help in the rescue of 100 survivors.

The whales were refloated at high tide in the late morning but linked up with a so-called "super pod" of another 200 whales gathered off shore.

Rescuers waded into neck-deep water, defying a shark threat to form a human wall and guide the survivors out to sea while also prevent the other 200 from coming to shore.

"But in spite of best efforts by everyone to prevent further losses, the large pod of approximately 200 pilot whales that were free-swimming, have stranded," DOC spokesman Herb Christophers said.

"We may salvage some of the stranded whales. Not all stranded whales can successfully be refloated.

"Even when some whales are saved, they may still restrand as has happened in this instance and prolongs the effort and reduces the chances of success."

About 20 whales who restranded earlier in the day were euthanised "out of concern for their welfare," Christopher added.

The whales beached at low tide, three kilometres (1.8 miles) from where the first group had died Friday.

"We don't know why the super pod came in," said Daren Grover, the general manager of environmental group Project Jonah which is assisting with the rescue.

"They may have been picking up some calls from the whales here and come in to respond. It's very unusual, not something we have seen before."

DOC ranger Mike Ogle told Radio New Zealand the whales could have been frightened into the shallows by a shark.

One whale had been found with bite wounds and great white sharks were known to be in the area off Farewell Spit, he said.

"There's one carcass out there with some shark bites in it - but not a big one, just a small one, but quite fresh bites so yeah, there's something out there."

Hundreds of volunteers mobilised to help the rescue operation with many working to comfort the stranded animals and keep them cool in the morning heat while they waited to refloat them on the high tide.

Tim Cuff, a marine mammal medic with Project Jonah, told the New Zealand Herald of emotional scenes over the mass deaths.

"It's a pretty sad scene up on the beach where there's a long line of dead whales," he said.

"One German girl didn't really want to leave her whale. She was crying and had her hand on it."

DOC officials said the carcasses would either be tethered and towed out to sea, or left to decompose in the sand dunes.

Farewell Spit, about 150 kilometres (95 miles) west of the tourist town of Nelson, has witnessed at least nine mass beachings in the past decade.

Pilot whales grow up to six metres (20 feet) long and are the most common species of whale in New Zealand waters.