About 300 whales will be moved with a digger and buried in the sand dunes further up Farewell Spit, South Island.
On Monday, conservation workers pierced the bodies to release gas built up during decomposition, following warnings the carcasses might explode.
It is not clear why the whales continue to arrive on the beach.
"It has been decided it is more suitable to take the dead whales out of the area that is open for public walking access," New Zealand's department of conservation said on its website.
Last week, more than 400 whales arrived on the 5km-long (three mile-long) stretch next to Golden Bay, in one of the worst beaching incidents in New Zealand's history. Most of the them died, while some were successfully floated back out to the sea by conservations officials and volunteers.
Since then, more whales have also come ashore, including more than 200 on Saturday, who later mostly refloated on a high tide and returned to sea.
But Department of Conservation spokeswoman Trish Grant told the BBC that that group was still swimming worryingly close to shore.
"We have staff in a boat offshore because there is a risk they could re-strand," she said.
Stressing the difficulty of preventing whales from stranding themselves, she added that "if they start to move towards shore... sometimes we can get people in the water to try and deter them".
New Zealand has one of the highest stranding rates in the world. About 300 dolphins and whales end up on beaches in the country every year, according to Project Jonah.
Many of these incidents happen at Farewell Spit. In February 2015 about 200 whales beached themselves at the same location, of which at least half died.
New Zealand authorities have said they will move the carcasses of hundreds of whales that died in a mass stranding to an area not open to the public.