UPDATED 4.13PM Rescuers trying to save 100 whales who survived one of the country's largest mass strandings are facing a major setback as the refloated whales start heading back into the beach.

Fifty of the refloated whales have headed back to shore at the northern end of Golden Bay. 

WATCH ABOVE: Steve Whitehouse technical advisor of Whale Rescue joins Laura McGoldrick to discuss this disaster 

Only 100 pilot whales survived after a large pod of 416 stranded on Farewell Spit overnight.

The Department of Conservation Golden Bay operations manager Andrew Lamason said the survivors that had been refloated were now swimming in the wrong direction and headed back into the bay.

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

Lamason said they would not have another chance to refloat the whales until tomorrow's high tide as it was too dangerous to try a rescue at night.

A whale rescue expert is dumbfounded conservation department crews weren't stationed earlier at the site

DoC said it received a report a pod looked like it might beach at 8pm yesterday.

Project Jonah and the local community were alerted about the possible stranding and scores of volunteers were mobilised at first light to try to save the stricken mammals.

Project Jonah issued a Facebook alert about the mass stranding. Hundreds of people have responded to the call for volunteers and the road to the South Island beach is 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.

Those keen to take up the offer had to present their Project Jonah ID card and call customer services on 0800 802 802 for a booking.

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

Rescue efforts were focusing on refloating the remaining 100 live whales at high tide, which was at 10.30am.

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.

Ogle urged as many people as possible to help refloat the surviving whales.

Those helping in the rescue were also told to come prepared with wetsuits, food and water.

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."

A team of up to 30 trained medics were headed to the stranding and the call had gone out for volunteers across the region to help.

Six years ago 70 pilot whales stranded in the same area, also in February. The whales, who became separated from their pod, were successfully refloated.

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

- NZ Herald