The mercury rose to 45C (113F) in Sydney's western suburb of Campbelltown on Sunday.
Wildlife officials said hundreds, if not thousands, of flying fox bats fell from trees after falling victim to the intense heat.
Campbelltown flying fox colony manager Kate Ryan told the local Camden Advertiser: "They basically boil... their brain just fries and they become incoherent.
"It would be like standing in the middle of a sandpit with no shade."The flying fox is Australia's largest bat and is listed as a "vulnerable" species nationally with its survival ranked as a "critical priority" under local laws.
New South Wales Wildlife Information, Rescue and Education Service (WIRES) said losses of bats to the brutal conditions could run into the thousands.
Rescuers were able to save the lives of more than a hundred of the animals, but many scattered across the ground did not survive and others died still clinging to trees.Sydney recorded its hottest day since 1939 on Sunday when the suburb of Penrith reached 47.3C (117F).
Players were forced off the court at Sydney International tennis tournament due to the extreme weather conditions.
It comes after researchers warned that climate change means more than 99% of green sea turtles in some areas of the Great Barrier Reef are now female.
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