Experts fear between 200 and 350 koalas died when the Crestwood-Lake Cathie fire ripped through crucial koala habitat.
Just over two thirds of the fire ground footprint is prime koala habitat.
The koalas in that area are of national significance due to their genetic diversity.
The extent of the impact will start to become clear from today (October 31).
A team from Port Macquarie Koala Hospital, along with representatives from Port Macquarie-Hastings Council, are now assessing the burnt-out area.
They will assess the impact and rescue injured koalas and other injured wildlife.
A line search will be conducted as part of the process.
Injured koalas will be taken to Port Macquarie Koala Hospital and other injured animals passed on to FAWNA.
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Koala Conservation Australia president Sue Ashton said the koalas in that area were a genetically diverse group which made them really rare.
"That means they can adapt much more to changes like climate change and change of habitat," she said.
The bushfire which continues to burn in the area of Lake Innes and Lake Cathie, south of Port Macquarie has burned more than 2550 hectares, including an important koala breeding ground.
Mrs Ashton told AAP the loss was a "tragedy".
"The beauty of this particular population is that it's so genetically diverse that it's of national significance," she said.
"A lot of the koalas are being mixed and cross-bred now so to lose a large part of that population is very devastating."
The Lake Innes Nature Reserve, Innes Peninsula and the area towards Lake Innes Drive is known as a koala hub or the engine room.
Genetic diversity is important when it comes to koala population health and resilience.
The koala losses come at a time when the koala population is already in decline.
"We are losing them at a much faster rate than they are breeding and they are in real decline," Mrs Ashton said.