Hope for the survivors of one of New Zealand's largest ever whale strandings is "slowly slipping away'', with Farewell Spit a scene scattered with the distressed and dead.

The Department of Conservation said about 416 pilot whales stranded near the base of Farewell Spit, Golden Bay, overnight, of which 250 to 300 were already dead when the whales were discovered early this morning.

Fifty of the 100 refloated pilot whales have since restranded themselves. The stranding is New Zealand's third biggest on record.

At 8.30pm, a DoC spokesman said the crew of hundreds of volunteers - made up of Project Jonah, DoC authorities and ordinary members of the public - had been withdrawn for the night.

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No one would be allowed to stay in the water overnight, as it would be too dangerous.

"We'll wait for the morning,'' the spokesman said.

People would be back at the site early tomorrow morning and an official update would be made available at 7.45am, he said.

Earlier, Takaka DoC operations manager Andrew Lamason said some of the whales were looking "very distressed" as many "slowly slipped away".

"There are about 50 whales offshore, but they're not looking great out there, just milling around.

"If you were going to design a geographical trap for whales, Golden Bay is pretty much perfect."

He said there were about 80 to 90 whales still alive on the beach.

"There are a lot of volunteers, a lot of tourists ... we'll ask people to leave the beach at about 8.30pm and leave the whales in peace."

More than 500 volunteers have helped in the rescue effort.

He said the survivors that had been refloated swam in the wrong direction and headed back in to the bay this afternoon.

Rescuers had fingers crossed they would still turn around on the high tide but were preparing for the worst.

Lamason said efforts to refloat the surviving whales would begin again tomorrow morning, because it was too dangerous to try a rescue at night.

Professor Liz Slooton, of the University of Otago's department of zoology, told the Herald there was a wide range of causes for whale strandings.

She said whales may beach themselves because they were sick, dying, giving birth or disoriented.

While natural causes such as earthquakes and storms could be a factor, human causes, including noise, may lead to a whale beaching itself, Slooton said.

Slooton earlier told the Herald it was "remotely possible, but unlikely" seismic testing had caused the mass stranding.

"Most whale strandings are of one or two individuals, or a small group, which makes it much easier to figure out what caused the stranding," she said.

"With a mass stranding like the one at Farewell Spit - usually only one or two individuals are sick or in trouble."

She said the rest of the pod would not leave the area because whales had "very strong social bonds".

Pilot whales were normally found in water several hundred metres deep, and often more than 1000m deep, Slooton added.

She said the layout of the Farewell Spit, an area known for whale strandings, did not help.

"Pilot whales - also sperm whales and beaked whales - are not very familiar with shallow water.

"The large areas of very shallow water near Farewell Spit will be confusing for several reasons. It will be difficult for the whales to figure out which way they need to swim to find deeper water as it's shallow over such large areas."

On a "normal" stretch of coastline the whales would not have to go far to find where the water got deeper, she said.

"Echo-location doesn't work all that well in shallow water. Rather than bouncing back nicely - like off a wall - the sound will tend to bounce away from the whales, with a much smaller proportion of the signal bouncing back."

DoC ranger Kath Inwood said previously whale carcasses had been either dropped on the dunes back from the beach, or tethered and taken out to sea to naturally decay.

"With the large number involved in this stranding, consideration will need to be given to practical options for dealing with the carcasses, and keeping them in the ecosystem," she said.

Lamason earlier said Project Jonah had done some great work helping with today's rescue.

"Project Jonah has been doing a fantastic job organising the volunteers, providing instruction and safety briefings, and even managing the car parking issues."

Rescuers are working hard to refloat the surviving whales. Photo / Tim Cuff
Rescuers are working hard to refloat the surviving whales. Photo / Tim Cuff

In the meantime volunteers were helping DoC staff care for the stranded whales throughout the afternoon and doing whatever they could to keep them comfortable, he said.

Minister of Conservation Maggie Barry thanked DoC staff and volunteers helping to refloat the whales.

"Project Jonah, local volunteers and DoC staff, led by Andrew Lamason, have been working hard to save the whales and I really want to commend them for their heroic efforts.

"It is terribly sad to see these magnificent creatures in this state and distressing and traumatic for the volunteers to see the hundreds of dead whales on the beach."

Project Jonah earlier issued a Facebook alert about the mass stranding at the northern end of Golden Bay. Hundreds of people responded to the call for volunteers and the road to the South Island beach was packed with cars heading to the remote area.

The Interislander ferry this morning offered free passage on its afternoon sailings for marine mammal medics headed to the rescue operation.

Project Jonah said 75 per cent of the whales were dead when rescuers arrived at first light.

Some of those that survived the night stranding were already able to swim on their own.

DoC spokesman Mike Ogle said the whales had stranded on the inside beach of Farewell Spit, 1km from Triangle Flat, near Puponga.

Project Jonah general manager Darren Grover said he was told last night a large pod of pilot whales had been spotted close to shore and it was feared they may beach overnight.

"We were told by DoC there may well be whales on the beach this morning."

Specialists from Massey University would be doing necropsies on some of the dead whales later today.

It's the third largest recorded whale stranding in New Zealand since the 1800s. A thousand whales were stranded on the Chatham Islands in 1918 and 450 in Auckland in 1985.

Six years ago 70 pilot whales stranded on Farewell Spit, also in February. The whales, which became separated from their pod, were successfully refloated.

In December 2006, 140 pilot whales stranded at Puponga Bay. Most were saved.

A deadly season for whales


The deadliest months for whales beaching themselves at Farewell Spit is from November to March, according to DoC.

Stranding "hotspots" include two beaches on the Chatham Islands, the Coromandel, Northland, Kaipara and Stewart Island.​

Recent Farewell Spit strandings include;

February, 2015: 98 pilot whales stranded.

January, 2014: About 70 whales strand themselves.

January, 2014: Nine whales are euthanised after beaching themselves twice.

November, 2012: 28 pilot whales stranded at the high-tide mark.

January, 2012: More than 80 whales die after a mass stranding of 99 pilot whales.

What to do in a whale stranding

• Stay away from a whale's tail at all times.
• Keep whales wet using light cotton sheets and pouring water on the whale.
• Do not pour water down the whale's blowhole - they breathe through it.
• Call for help as soon as you find a marine mammal in distress.