Other winners included start-up company v2food for commercialising research in plant-based meat alternatives; an investment tool for transport logistics in road and rail freight; understanding water resources in Northern Australia; and the Eureka Prize-winning Indigenous STEM Education project.
CSIRO Chief Executive Larry Marshall said this year's awards were particularly poignant, and thanked the organisation's many partners, customers, and supporters through the tough year.
"This year has tested every one of us, professionally and personally, and every day I have been in awe of our people's determination to make life better for Australia despite unprecedented disruption," Dr Marshall said.
"All of our finalists today demonstrate the depth and breadth of impact we've had this year, at a time when Australia has needed its national science agency most – and will need us more than ever in the years ahead as we recover from this pandemic.
"CSIRO has demonstrated why Australia's high levels of trust in us are so well placed, and we come to work every day to continue to deserve that trust."
Minister for Industry, Science and Technology Karen Andrews congratulated CSIRO with an "almighty thank you".
"I think it is impossible to overstate the gratitude we all have for your work in what's been an extraordinary year," Minister Andrews said.
"Our black summer of devastating bushfires and the COVID-19 pandemic have reinforced just how central science is to our very survival.
"In those times of turmoil, we have turned to our scientists, particularly you at the CSIRO, to help shine a light on the unknown and map a path for the future.
"CSIRO is truly a national treasure. And over the last twelve months you've deepened the trust of the Australian people that are looking to science to light a way forward.
"I am grateful for all your hard work, and on behalf of a grateful nation, I again say thank you."
Full list of 2020 CSIRO Award winners:
The Chairman's Medal for Science and Engineering Excellence
For scientific excellence in foresight, concept, development and rapid delivery of a challenge model and evaluation of candidate vaccines along with associated research, to exacting standards for licensing, in the face of the COVID-19 pandemic.
The Sir Ian McLennan Impact from Science and Engineering Medal
For pioneering research towards the Transport Network Strategic Investment Tool (TraNSIT) and revolutionising the way Australia's transport-related infrastructure investments are prioritised, together with partners at the Department of Infrastructure, Transport, Regional Development and Communications, and acknowledging Anthony Carlson for his support.
The CSIRO Entrepreneurship Award
For a highly successful entrepreneurial approach to create the v2food start-up company to develop and commercialise innovative plant-based meat alternative products.
The CSIRO Collaboration Medal
For the collaboration necessary to successfully deliver the most extensive, multi-disciplinary water and agricultural assessment of its kind in the world, together with partners at the Department of Infrastructure, Transport, Regional Development and Communications.
For their rapid and collaborative efforts to conduct critical research and manufacturing work in pursuit of a potential COVID-19 vaccine, together with partners at CSL, University of Queensland, and Coalition for Epidemic Preparedness Innovations (CEPI).
The Aboriginal and Torres Strait Islander Engagement Impact Excellence Medal
For working in partnership with schools and communities to establish best practice education models that increase participation, aspiration and achievement of Aboriginal and Torres Strait Islander students and communities in science, technology, engineering and mathematics.
The CSIRO Medal for Lifetime Achievement
The Chief Executive Team CSIRO Award
The CSIRO HSE Medal for Area Custodian of the Year
Australian National Insect Collection (ANIC) Ethanol Collection Relocation Team
CSIRO Alerts Notification Service Project Team
The CSIRO Medal for Support Excellence
Flattening the Response Curve
The CSIRO Medal for Diversity and Inclusion
Domestic family violence and abuse working group
The John Philip Award for the Promotion of Excellence in Young Scientists and Engineers
The Delia Muller Aboriginal and Torres Strait Islander Study Award
The Chief Executive Professional Development Award