| Organisation | Year range | Notes |
| Commonwealth, by portfolio |
| Attorney-General's Department | 2008–2011 | |
| Criminology Research Council | 2008–2011 | |
| Department of Agriculture, Fisheries and Forestry | 2008– | |
| Australian Centre of Excellence for Risk Analysis | 2008–2009 | |
| Australian Weeds Research Centre | 2010 | |
| Centre of Excellence for Biosecurity Risk Analysis | 2013– | |
| Department of Broadband, Communications and the Digital Economy | 2008–2009 | |
| Department of Climate Change and Energy Efficiency | 2011– | Est. 2007 |
| National Climate Change Adaptation Research Facility | 2012– | Established in 2008 |
| Department of Defence | 2008–2010, 2013 | Scheme was moved from DPMC to DOD in 2013 |
| Army History Unit | 2008–2010 | |
| Department of the Prime Minister and Cabinet | 2011–2012 | |
| Department of Families, Housing, Community Services and Indigenous Affairs | 2008– | |
| Department of Foreign Affairs and Trade | 2008– | |
| AusAID | 2008– | |
| Australian Centre for International Agricultural Research | 2008– | |
| Department of Health and Ageing | 2008– | |
| Australian Centre for Hepatitis and HIV Virology Research | 2008–2010 | See similar organisation under non-commonwealth |
| Australian National Preventive Health Agency | 2012– | Est. 2011 |
| Cancer Australia | 2008– | |
| National Health and Medical Research Council | 2008– | |
| Australian Health Ministers Advisory Council | 2008– | |
| International Cancer Genome Consortium | 2010– | |
| National Asbestos Centre | 2008–2010 | |
| National Institute of Clinical Studies | 2008– | Incorporated into the National Health and Medical Research Council (NHMRC) in 2007 |
| Department of Industry, Innovation, Science, Research and Tertiary Education | 2008– | |
| Australian Institute of Aboriginal and Torres Strait Islander Studies | 2008–2010 | |
| Australian Research Council | 2008– | |
| Commonwealth Scientific & Industrial Research Organisation | 2008– | |
| CSIRO Flagship Collaboration Fund | 2008– | |
| Office for Learning and Teaching | 2013– | |
| Department of Infrastructure, Transport, Regional Development and Local Government | 2008–2009 | |
| Australian Transport Safety Bureau | 2008 | |
| Department of the Prime Minister and Cabinet | 2008, 2010–2012 | Scheme was moved from DPMC to DOD in 2013 |
| National Security Science and Technology Unit | 2008 | |
| Department of Resources | 2012– | |
| Australian Renewable Energy Agency | 2012– | See below – Previously on the register as Non-commonwealth, under name Australian Solar Institute |
Department of the Environment, Water, Heritage and the Arts/
Department of Sustainability, Environment, Water, Population and Communities | 2008– | |
| Australian Antarctic Division | 2008– | |
| Australian Marine Mammal Centre | 2008– | formerly the Australian Centre for Applied Marine Mammal Science |
| Australian Biological Resources Study | 2008– | |
| Commonwealth Environment Research Facilities | 2008– |
| Marine and Tropical Sciences Research Facility | 2008– | Core program funding 2006– 2010 |
| Great Barrier Reef Marine Park Authority | 2008–2010 | |
| National Centre for Vocational Education Research | 2008– | Was run under DEEWR 2008–2010 |
| Australian Treasury | 2012– | |
| Rural Research and Development |
| Australian Egg Corporation | 2008– | |
| Australian Pork | 2008– | |
| Australian Wool Innovation | 2008–2009, 2011– | |
| Cotton Research and Development Corporation | 2008– | |
| Dairy Australia | 2008– | |
| Fisheries Research and Development Corporation | 2008–2013 | |
| Forest and Wood Products Australia | 2008– | |
| Grains Research and Development Corporation | 2008– | |
| Grape and Wine Research and Development Corporation | 2008– | |
| Horticulture Australia | 2008– | |
| Land and Water Australia | 2008–2009 | |
| Meat and Livestock Australia | 2008– | |
| Rural Industries R&D Corporation | 2008–2009, 2011– | |
| Sugar Research and Development Corporation | 2008– | |
| Non-Commonwealth |
| Alcohol Education and Rehabilitation Foundation | 2008–2010 | |
| Alzheimer's Australia Dementia Research Foundation | 2012– | |
| Arthritis Australia | 2008–2010 | |
| Australian Centre for HIV and Hepatitis Virology Research | 2011– | Administered by University of Melbourne. See similarly named organisation previously listed under Department of Health and Ageing |
| Australian Coal Research (Australian Coal Association) | 2008– | The Australian Coal Association Research Program was established in January 1992. |
| Australian Housing and Urban Research Institute | 2008– | |
| Australian Institute of Nuclear Science and Engineering | 2008– | |
| Australian National Low Emissions Coal Research and Development | 2011– | |
| Australian Primary Health Care Research Institute | 2008– | Administered by Australian National University |
| Australia and Pacific Science Foundation | 2010 | |
| Australian and New Zealand College of Anaesthetists | 2008–2010, 2012– | |
| Australian Rotary Health | 2008– | |
| Australian Solar Institute | 2010–2011 | See above |
| Australian Stem Cell Centre | 2008–2012 | |
| Australian Water Recycling Centre of Excellence | 2011– | |
| Brain Foundation | 2008–2010 | |
| Brown Coal Innovation Australia | 2012– | |
| Bupa Foundation | 2011– | |
| Cystic Fibrosis Australia | 2008–2010 | |
| Dairy Innovation Australia | 2008– | |
| Diabetes Australia Research Trust | 2008, 2010– | |
| Diabetes Vaccine Development Centre | 2008 | |
| The Garnett Passe & Rodney Williams Memorial Foundation | 2008– | |
| Geoffrey Gardiner Dairy Foundation | 2008– | |
| The Financial Markets Foundation for Children | 2008– | |
| HCF Health and Medical Research Foundation (HCF Health Insurance) | 2011– | |
| The Hermon Slade Foundation | 2008–2010 | |
| Inner Wheel Australia | 2010 | |
| JO & JR Wicking Trust | 2008–2010 | |
| The Judith Jane Mason and Harold Stannett Williams Memorial Foundation | 2008–2010, 2012– | |
| Juvenile Diabetes Research Foundation | 2008– | |
| Kidney Health Australia | 2008–2010 | |
| Leukaemia Foundation | 2008– | |
| MBF Foundation | 2010 | |
| Motor Neurone Disease Research Institute of Australia | 2009– | |
| Multiple Sclerosis Research Australia | 2008–2010 | |
| National Breast Cancer Foundation (Australia) | 2008– | |
| National Centre of Excellence in Desalination | 2011– | |
| National Food Industry Strategy | 2008 | Disestablished in 2008 |
| National Heart Foundation of Australia | 2008– | |
| Ophthalmic Research Institute of Australia | 2008–2010 | |
| Pfizer Australia | 2008– | |
| Pharmacy Guild of Australia | 2008–2009 | |
| Prostate Cancer Foundation of Australia | 2010– | |
| RANZCO Eye Foundation | 2008–2010 | |
| Sea World Research & Rescue Foundation | 2008–2010 | |
| Science & Industry Endowment Fund (SIEF) | 2011– | |
| Sylvia and Charles Viertel Charitable Foundation | 2008– | |
| VicHealth | 2011– | |
| Victorian Department of Education and Early Childhood Development | 2012– | |
| Victorian Department of Health | 2013– | |
| Workers Compensation Dust Diseases Board of New South Wales | 2009– | |
