More than 400 whales beached themselves in a mass stranding at the sandspit at the northern end of Golden Bay on Thursday night.
About 300 died but the surviving 100 were successfully refloated at high tide about lunchtime today.
People have been warned to stay away from a beach where hundreds of whale carcasses are at risk of exploding.
The Department of Conservation has cordoned off the area in which hundreds of pilot whales became stranded late last week on Farewell Spit, at the top of the South Island.
Arrangements will be made within the next few days about how the bodies will be disposed of, but in the mean time, members of the public are being asked to stay away from that side of the beach for health and safety reasons.
DoC spokesman Herb Christophers told the Herald: "Because they're very warm, the decomposition is very rapid in their gut. What happens is their stomach swells up and they do explode.
"I know this from first-hand experience...having seen a sperm whale explode. It's not a pleasant thing to be around.
"The smell will be atrocious, but it's just part of the decomposition of the animals and they will be returned to Papatuanuku (the earth) eventually, or Tangaroa (the sea).''
Exactly how many whales became stranded over the last few days would be known some time this week, he said.
But Christophers estimated the total was around the 650-mark.
"Of those, I'm guessing nearly 50 per cent of them died. We lost 300 on the first day and a few others had to be euthanised.
"It's not easy to nail down these numbers.''
The warning came after good news yesterday, when 17 pilot whales stranded at Golden Bay yesterday morning were successfully re-floated with the help of volunteers and ordinary members of the public, including children.
About 200 of the 240 whales that were beached there on Saturday refloated themselves at high tide about 11pm. They are now swimming east towards Collingwood.
Volunteers discovered the whales had successfully got back into the water when they went down to the beach yesterday morning to continue their rescue effort.
The whales were from a different pod to the 416 whales stranded last Thursday night.
Hundreds of volunteers flocked to the scene, south of Puponga, to help DoC rangers and Project Jonah medics refloat the remaining at the next high tide, about midday.
Rescuers hoped the whales would find their way into deeper, safer waters, a DoC spokeswoman said.
German visitor Lea Stubbe makes an emotional farewell to the pilot whale she cared for. Photo / Tim Cuff
The Department of Conservation thanked those who had travelled near and far to help in the rescue effort.
Christophers said authorities and volunteers had been overwhelmed by the support, which saw traffic jams over the last few days - something of a rare sight in the Golden Bay area.
They had also received offers of help from people in other parts of the country and as far as Australia and even a person who had contacted them from California, who indicated they were willing to get on a plane if they required more help.
