Rescuers believe there are no more live whales in the harbour, after an estimated 470 whales became stranded this week.
Authorities have revised the number of dead whales down to 350.
Marine Conservation Program biologist Kris Carlyon said on Saturday only one whale had restranded itself on Friday night, which was considered a success given 20 were rescued that day.
On Monday, around 270 whales were discovered at three sites in Macquarie Harbour. One-third were already dead before rescue efforts could begin.
A further 200 dead whales were spotted on Wednesday morning some 7-10 kilometres from the original site.
Efforts have begun to move the hundreds of carcasses out to deeper water using barges or towed by boats, which could take several days and relies on smooth conditions.
Authorities are experimenting with burying the dead whales at sea.
This week’s mass stranding surpasses the country’s previous 1996 record when around 320 pilot whales were stranded in Western Australia.
The cause of mass strandings is often unknown but experts suggest the whales may have been drawn into the coast to feed.