Many of the flying foxes, or fruit bats, fell dead from the sky while the carcasses of others hung on branches.
Local residents said the stench of decay was unbearable as temperatures reached nearly 110° F in Brisbane.
At least 16 people were reportedly receiving anti-viral treatment after coming into close contact with a bat.
The animals sometimes carry lyssavirus, which can cause paralysis and even death in humans.
But wildlife officials say the flying foxes are a key part of the ecosystem, and such a massive loss to their populations will have consequences.
“I don’t necessarily like the bats, but I don’t like seeing them dead,” Dayboro resident Murray Paas told Guardian Australia.
The Royal Society for the Prevention of Cruelty to Animals was caring for many young bats left orphaned by the heat disaster.