The Department of Primary Industries, Parks, Water and Environment are responding to reports a large pilot whale became stuck in the harbour near Strahan on Saturday afternoon.
Three smaller pilot whales, which were swimming with the large whale before it became stranded, also remain in the harbour.
The whales appear to be healthy and should be returned to sea on Sunday, wildlife biologist Sam Thalmann says.
"The harbour is a large, complex marine environment, with very dark waters and an intricate shoreline making detection of these whales difficult. However, once the whales are stabilised, we will make all efforts today to move these whales back out to sea," he said in a statement.
About 470 long-finned pilot whales were found beached on sandbars at Macquarie Harbour in late September—the biggest mass stranding on record in Australia.
After a week-long rescue effort, only 111 could be saved, leaving authorities the gruesome task of disposing of more than 350 carcasses.