It was one of the largest mass beachings recorded in New Zealand, where strandings are relatively common, said Andrew Lamason, the department's regional manager.
Some 416 pilot whales beached themselves overnight at Farewell Spit in the Golden Bay region at the northern tip of South Island.
Lamason said about 70 percent had perished and attempts were underway to get the remaining whales offshore at high tide but the outlook was gloomy.
"With that number dead, you have to assume that the rest are in reasonably poor nick as well," he told Radio New Zealand.
"So we're sort of preparing ourselves for a pretty traumatic period ahead."
A department spokesman said there were so many whale carcasses in the shallows that it was difficult for the volunteers to get living animals back into the water.
"The dead ones that are floating around out there are obstructing their course out to sea," he told AFP.
"I understand they're concerned about people's welfare... there's quite a safety issue there."
He said most of the surviving whales had been refloated and dozens of volunteers formed a human chain to try to stop them beaching again.
"We've got a line of people between the shore and the whales to screen them and stop them coming back in," he said.
"Hopefully the outgoing tide will take them out to sea and they'll swim away."
Pilot whales are renowned for tragically swimming back ashore after being refloated in an apparent attempt to rejoin their pod.
Rescuers work to refloat the whales. Source: Facebook/Project Jonah New Zealand
By Friday afternoon, 50 of the 100 re-floated pilot whales had restranded themselves after attempting to return to the beach.
The department said the initial incident was the third biggest mass stranding on record in New Zealand.
The biggest occurred when 1,000 whales beached at the remote Chatham Islands in 1918, followed by 450 that washed ashore in Auckland in 1985.
Pilot whales grow up to six metres long and are the most common species of whale in New Zealand waters.
Farewell Spit, about 150 kilometres (95 miles) west of the tourist town of Nelson, has witnessed at least nine mass strandings of the species in the past decade, although the latest is by far the largest.
Lamason said the reason the whales beached themselves was unknown but he believed it was partly due to the local geography.
"If you designed something to catch whales then Golden Bay is probably the perfect design," he said.
"Out at Farewell Spit it's a big massive sweeping hook of sand coming about, the bay is very shallow and once the whales get in there... it's very difficult to work out which way is out."
