The alleged killings followed a spate of animal mutilations in Victoria state involving native species including the kangaroo, wallaby and koala.
The flying fox, Australia's largest bat, is listed as a "vulnerable" species nationally with its survival ranked as a "critical priority" under local laws.
Rescuer Sammy Ringer said she was alerted to the deaths last week when a local resident in Conondale, a small town in the south of Queensland state, heard some shots being fired.
"As we got further into the colony, there was a pretty horrendous smell of bats that had been shot previously," she told the Australian Broadcasting Corporation Tuesday.
"They had been lying on the ground for maybe a week or two."
Ringer, leading a small group of people into the bush, said it was a "horrific scene" and "we kept coming across more dead bats".
The rescuers tried to help baby bats whose mothers had been killed but only two were able to be saved, she added.
The maximum penalty for killing 10 or more grey-headed flying foxes is Aus$126,150 (US$96,000) or a year behind bars, the department added.
The RSPCA's Queensland branch said up to 50 bats were believed to have been killed, adding it was involved in the investigation as there was "considerable suffering" for the bats before they died.
"We are talking about obviously animals that weren't killed instantly. There were babies that were still alive with dead mothers," RSPCA spokesman Michael Beatty told AFP.
"People need to be aware that the flying foxes are protected... without flying foxes there would be no pollination in the forests."
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)