In total, more than 650 pilot whales have beached along a 5km stretch of coastline over two days on Farewell Spit, at the tip of the South Island.

About 335 of the whales are dead, 220 remain stranded and 100 are back at sea.

Department of Conservation Golden Bay operations manager Andrew Lamason said rescuers are sure this is a new pod because they had tagged all the refloated whales from the first group.

The news was devastating for hundreds of volunteers who came from around the country to help with the initial group of 416 stranded whales that was found early on Friday, many of them already dead.

Volunteers are planning to return on Sunday to help refloat as many healthy whales as they can.

Mr Lamason said about 20 of the new group were put down by conservation workers because they were in poor condition and more would likely need to be treated that way.

Rescuers had been hopeful earlier on Saturday after efforts to refloat the initial group of whales had gone well, following a frustrating day on Friday.

Mr Lamason said improved weather and clear water helped the rescue attempt.

He said about 100 surviving whales from the initial group were refloated, and dozens of volunteers formed a human chain in the water to prevent them from beaching again.

He said volunteers were warned about the possibility of stingrays and sharks, after one of the dead whales appeared to have bite marks consistent with a shark. He said there had been no shark sightings.

Officials will soon need to turn to the grim task of disposing of hundreds of carcasses.

Mr Lamason said one option was to tether the carcasses to stakes or a boat in the shallow tidal waters and let them decompose.

The problem with towing them out to sea or leaving them was that they could become gaseous and buoyant, and end up causing problems by floating into populated bays.

Farewell Spit, a sliver of sand that arches into the Tasman Sea, has been the site of previous mass strandings.

Sometimes described as a whale trap, the spit's long coastline and gently sloping beaches seem to make it difficult for whales to navigate away from once they get close.

New Zealand has one of the highest rates of whale strandings in the world, and Friday's event was the nation's third-biggest in recorded history.

The largest was in 1918, when about 1,000 pilot whales came ashore on the Chatham Islands. In 1985, about 450 whales stranded in Auckland.