Parks and Wildlife Service wildlife biologist Dr Kris Carlyon said on Thursday afternoon a total of 88 whales had been rescued and returned to deeper water.

"[To rescue] 90 is a fantastic result for us. We are really, really pleased with that," Dr Carlyon said.

Incident controller Nic Deka said more whales had been identified as being "viable" for rescue and they were optimistic about conditions on Thursday evening and Friday morning.

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Dr Carlyon said the whales were "on their own" once they had been towed out to deeper water, but previous studies showed it was likely they would regroup.

"We get them into deep water outside the gates of Macquarie Harbour and then they're really on their own. It's up to them to work it out," Dr Carlyon said.

"Tracking work in the past has shown that animals which are released individually do reform their pod after a period of time and then behave as we would expect.

"We're hoping that is what is happening out at sea and that they are... reforming those pods."

Mr Deka said while the rescue effort of the whales which remained alive was continuing, efforts and focus were beginning to shift to how the carcasses of the estimated 380 dead whales would be removed and disposed.

Mr Deka said the plan was still being developed alongside expert help from the CSIRO and with the assistance of the local aquaculture companies.

He said it was difficult to estimate how long the process would take, but he was optimistic a method could begin being implemented as early as Friday.

He said possible methods included loading the carcasses onto a barge or gathering the dead whales together to be towed out to sea.

They were also working to contain the dead whales in single locations with pens or weighted buoys so they were not spread about the harbour by the tides and currents.