More than 20 cases of Hendra have been reported in horses in Queensland and New South Wales since June. In all cases, the horses either died or were euthanised.
Queensland scientists, in what is an Australian first, are fitting the bats with GPS data loggers in an effort to find out where they are going and what they're up to.
Queensland's agriculture minister, Tim Mulherin, said the technology was being used as part of a range of ongoing Hendra Virus research in the state.
"When attached to a flying fox, the GPS data loggers tell us whether the bat is feeding, sleeping or flying, and where it is flying to," Mulherin said.
"This will help us better understand movement between colonies, which in turn helps modeling when looking at the spread of Hendra virus between bat populations.
"By researching flying fox movements we can provide a clearer picture of why there are more confirmed cases of Hendra virus in some years and during certain months.
"This technology will allow us to measure movement to a very fine degree over a period of weeks, to build up a detailed picture of animal movements at a regional level," he said.
"We acknowledge there is much more research needed to understand the virus."
The state government, he said, was providing the funding needed for scientists to accelerate research.
"This ongoing Hendra virus research builds on our knowledge that bats are a natural reservoir for the virus and its presence is widespread but fluctuates throughout their populations.
"Each incident we deal with helps increase our knowledge base about this disease.
"We need to ensure we are working toward a safer environment for horse owners, vets and the community.
"Using cutting-edge technology such as these GPS data loggers helps us to achieve this goal," he said.
Queensland scientists have previously used the technology overseas while co-leading flying fox movement behaviour research for the United Nations Food and Agriculture Organisation in The Philippines.
Current Hendra Virus research includes: