The system comprises a detection tool (EpiDefend) and a forecasting tool (EpiFX) that use health and environmental data to produce a near real-time assessment of the likely presence of disease and how it might continue to spread.
Minister for Defence Industry Christopher Pyne congratulated the scientists and said the awards recognised a unique capability.
"This is an exciting development, which aims to predict the outbreak of disease so appropriate health management and prevention measures can be put in place," Minister Pyne said.
“Last year in Australia, we had over 230,000 confirmed cases of influenza, which costs the economy millions of dollars each year. Besides providing a forecasting capability for public health authorities, the innovative system can be used by Defence to protect troops against biological threats and pandemics.
"If we can reliably predict the impact of a seasonal epidemic, we can allocate medical support and resources more effectively to minimise its impact."
For the past two flu seasons, the system has been available to health authorities in Queensland, NSW and Victoria to inform their weekly influenza forecasts.
"Soon this revolutionary system could be extended to other states, potentially providing Australia’s first national disease surveillance and prediction system," Minister Pyne said.
"This is a significant innovation not benefiting Defence but the wider Australian community."
The system was awarded both the CIVSEC 2018 National Innovation Award and CIVSEC 2018 Award for Disaster Relief, Emergency Management and Humanitarian Services.
The Defence scientists recognised were Dr Tony Lau, Dr Peter Dawson, Dr Alex Skvortsov and Dr Ralph Gailis, along with University of Melbourne co-researchers Professor James McCaw and Dr Rob Moss.