There are roughly 20 whales still stranded and fighting for life on the sandbars but their chances of survival are becoming increasingly slim.
Wildlife biologist Kris Carlyon said four would have to be euthanised for welfare reasons.
"These are animals that we've given a chance. We've tried to release them, they haven't done well," he said.
Crews are now faced with the grim task of collecting carcasses, which are likely to be disposed of at sea if conditions allow.
"As the whales start to decompose, they will bloat and float and with wind and tide, they'll drift," Mr Deka said.
"They could cause a significant navigation hazard if we don't contain them."
Source: SBS News: Sarah Maunder
Wildlife Biologist Sam Thalmann said rescuers had experienced challenging conditions at Macquarie Harbour but had been "very lucky" in being able to free around 70 mammals.
"It's hard work, it's dynamic, it's challenging, but the rewards as we have seen over the last few days with over 70 animals released are great and they're very much worth the effort," he told reporters on Thursday morning.
"We've been very lucky over the last few days, we've had favourable tides ... but it is still very rough, and the animals do have to traverse quite a bit of broken water."
Source: POOL The Advocate
Cold and wet weather is expected on Thursday, ideal for the healthy whales but physically demanding on rescuers.
"It is challenging for volunteers and staff out there. It is emotional, there are animals swimming around, they're vocalising, and we can see the bonds and the pairings within them," Mr Thalmann said.
"We try to focus on the rewards when we do get those animals out."
Local salmon farmer Tom Moutney is one of the volunteers who joined the rescue effort, bringing along three boats.
"It's a pretty tight-knit community, we heard about it straightaway and offered to help, and do what we can," he told SBS News on Wednesday.
"We got here at about 7 o clock this morning with a couple of boats from Petuna, and we've just been moving whales as quick as we can."
While conditions have been tough, he said the morale among rescue crews has been strong.
"It's pretty positive, we're just doing what we can, every one we get is a win," he said.
Australia's largest stranding
Dr Carlyon said the stranding was definitely the biggest in Tasmania and likely the largest on record in Australia.
It surpasses Tasmania's largest mass stranding of 294 long-finned pilot whales in 1935 at Stanley.
It is also greater than a 1996 event where 320 pilot whales became beached at Dunsborough in Western Australia.
One large group was initially discovered stranded near the harbour's head on Monday, with rescuers on Wednesday morning spotting 200 dead whales a few kilometres away.
It is thought the two groups were part of the same pod.
"Pilot whales are incredibly social and maintain strong social bonds with each other and have been known to be found in groups up to 1,000," marine scientist Dr Vanessa Pirotta said.
"The ability for them to stick together and follow the leader is something we see often with these animals, which is why it is so heartbreaking."
The freed whales were likely to reform their social group, Dr Carlyon said.
Additional reporting: Sarah Maunder, Naveen Razik