Parts of Queensland, New South Wales and Victoria have been dealing with thousands of flying foxes over recent years, angering residents and worrying local councils.
Ecologist Dr Peggy Eby said despite the infestation, grey-headed flying foxes are listed as threatened because their numbers continue to decline.
At the weekend, around 30 bat pups were found dead at a park in Bega on the New South Wales south coast.
There have been similar reports elsewhere along the coast, including in the Hunter region.
Dr Eby said the deaths were taking place in Bundaberg, Queensland and all the way south into Melbourne, in Victoria.
She said it had been happening for two weeks, and there were a number of contributing factors.
"What we're seeing now is the effect on the animals of that loss of habitat — they simply don't have enough food," Dr Eby said.
"A lot of it is because of coastal development, but it's also due to clearing practices in rural areas.
She said the recent strong El Nino weather pattern had not helped either.
"Acute food shortages ... they're associated with spikes in El Nino, but with about a nine-month to 12-month delay," she said.
"There's no food for flying foxes or for other nectar-dependent wildlife.
"The mothers are going through a difficult nutritional phase, and they're reducing the amount of milk they're producing and the young starve.
"They hang on to the females for the first several weeks of life, when she flies form the roost at night, and they simply would lose the strength that they need to hold on."
'Human plague' eliminating crucial trees
Alexandra Seddon is a conservationist and wildlife carer from Merimbula on the New South Wales far south coast.
She said she had been caring for several rescued bats since last week.
"One lasted five days, but they're so terribly underweight because of the starving mothers," she said.
Ms Seddon said she had had calls from people reporting young distressed flying foxes.
"The plague of humans is eliminating more and more and more of the trees that they need," she said.
"Less and less food is available, even when it is a good flowering year, so they really are starving now and they're getting quite confused.
"They are desperate — really, really desperate and they're all terribly underweight this year."
Hugh Pitty from Friends of Glebe Wetlands in Bega said he had noticed the animals flying in search for food in a scattered pattern.
He said that suggested a lack of food.
"We have been concerned about habitat loss for quite a while," he said.
"It's the foraging habitat that's problematic when food becomes scarce, and then the heat just comes along and that's too much."