- MacDonald Wagner & Priddle Pty Ltd (1934 - 1980s)
- Macfarlane Burnet Centre - see Macfarlane Burnet Centre for Medical Research (1989 - c. 2000)
- Macfarlane Burnet Centre for Medical Research (1989 - c. 2000)
- Macfarlane Burnet Institute for Medical Research and Public Health (c. 2000 - )
- Machine Dynamics Pty Ltd (1972 - 1995)
- Mack Trucks Australia Pty Ltd (1963 - )
- Macquarie Island Station (1948 - ), Australian National Antarctic Research Expeditions
- Macquarie Textiles Group Limited (1869 - )
- Macquarie Worsteds Group (1957 - 1983)
- Management Investment Companies (1980s - )
- Manufacturing Industries Advisory Council (1958 - 1977), Commonwealth of Australia
- Marconi School of Wireless (1913 - 1980s), Amalgamated Wireless (Australasia) Ltd (AWA)
- Marconi's Wireless Telegraph Co Ltd (1900 - 1913)
- Marine and Freshwater Resources Institute (MAFRI) (1996 - ), Victorian Department of Natural Resources and Environment
- Maritime Wireless (1900s - c. 1914)
- Mary Kathleen Uranium (1954 - c. 1980)
- Masonite Corporation (Australia) Ltd (1938 - 1955)
- Massey Ferguson (Australia) Limited (1958 - )
- Materials Australia - see Institute of Materials Engineering Australiasia Ltd (IMEA) (c. 1999 - )
- Materials Research Laboratories (1974 - 1994), Defence Science and Technology Organisation (DSTO)
- Materials Technology Group, Swinburne University of Technology
- Mathematical Association of Western Australia (1958 - )
- Maunsell and Partners Pty Ltd (1957 - 1980s)
- Mauri Foods
- Mawson Station (1954 - ), Australian National Antarctic Research Expeditions
- Mayne Nickless Limited (1886 - 2002)
- McCoy Society for Research and Investigation (1935 - )
- Meat and Livestock Australia (1998 - )
- Meat Research Corporation (1991 - 1998), Commonwealth of Australia
- Medical Benefits Fund of Australia Limited (MBF) (c. 1947 - )
- Medical Equipment Control Committee (MECC) (1940 - 1947), Commonwealth of Australia
- Medical History Museum (1967 - ), The University of Melbourne
- Medical History Society of Victoria (c. 1953 - )
- Medicare Australia - see Health Insurance Commission (1974 - 2005), Commonwealth of Australia
- Medtel Pty Ltd (c. 1970 - )
- Melbourne and Hobson's Bay Railway Co (1854 - )
- Melbourne and Metropolitan Board of Works (1891 - 1990s), State of Victoria
- Melbourne Glass Bottle Works Company (1872 - c. 1915)
- Melbourne Hospital - see Royal Melbourne Hospital (1935 - )
- Melbourne Hospital (1848 - 1935)
- Melbourne Meat Preserving Company (1867 - 1880s)
- Melbourne Metropolitan Hospital Board
- Melbourne Milk Supply Company (1880? - )
- The Melbourne Technical College (1933 - 1954)
- Melbourne University Agricultural Society (1922 - ), The University of Melbourne
- Melbourne University Chemical Society (1904 - ), The University of Melbourne
- Melbourne University Engineering Students' Club (1889 - ), The University of Melbourne
- Melbourne University Medical Students' Society (1880 - ), The University of Melbourne
- Melbourne University Mining and Metallurgy Students' Society (1932 - ), The University of Melbourne
- Melbourne University Research Students' Association (1964 - ), The University of Melbourne
- Melbourne University Science Club (1888 - 1960s), The University of Melbourne
- Melbourne University Science Students' Society (1960s - ), The University of Melbourne
- Melbourne Woollen Mills
- Melbourne Zoological Gardens (c. 1857 - 1977)
- Menindee Lakes Scheme
- Mental Health Library, Office of Psychiatric Services, Charles Brothers Museum (1950s - 1989s)
- Mental Health Research Institute of Victoria (1956 - )
- Merck, Sharp and Dohme (Australia) Pty Ltd (1956 - )
- Metal Manufactures Limited (1916 - )
- Meteorological Branch/Bureau (1907 - 1955), Commonwealth of Australia
- Meteorological Society of New South Wales (1971 - )
- Meteorology CRC - see CRC for Southern Hemisphere Meteorology (1993 - 2000)
- Metrology Society of Australia (1993 - )
- Metropolitan Gas Company (? - 1950)
- Metropolitan Water, Sewerage and Drainage Board (1924 - 1987)
- Michell Australia Pty Ltd (1980s - )
- Microscopical Society of Victoria (1873 - )
- Microsurgery Foundation
- Military Research and Development Centre (MRDC)
- Miller, Milton & Ferris (Engineers) Pty Ltd (1970 - )
- MIM Holdings Ltd (1970 - 2003)
- Mineral Control Instrumentation Pty Ltd (1981 - 1996)
- Minerals Council of Australia (1995 - )
- Minerals Separation Ltd (1900s - )
- Ministry of Post-War Reconstruction (1944 - 1950), Commonwealth of Australia
- Mitchell, Giurgola & Thorp (1980 - 1990)
- Mittagong Creamery
- MM Cables Telecommunications (1988 - c. 2000)
- MM Electrical Merchandising (MMEM) (c. 1991 - )
- Mobil Oil Australia Pty Ltd
- Molecular Biology Unit (1981 - 1996), The Walter and Eliza Hall Institute of Medical Research
- Molecular Genetics of Cancer Division (1996 - ), The Walter and Eliza Hall Institute of Medical Research
- Molecular Plant Breeding CRC - see CRC for Molecular Plant Breeding (1997 - )
- Monash Engineering in Gippsland - see Gippsland School of Engineering (c. 1945 - 2003), Monash University
- Monash Institute of Medical Research (MIMR) (2005 - ), Monash University
- Monash Institute of Reproduction and Development (1991 - 2005), Monash Universuty
- Monash Medical Centre (1987 - )
- Monash University (1958 - )
- Monash University, Accident Research Centre (1987 - )
- Monash University, Australian Pulp and Paper Institute (APPI) (1989 - )
- Monash University, Centre for Advanced Materials Technology (1989 - )
- Monash University, Centre for Biomedical Engineering
- Monash University, Centre for Green Chemistry (2000 - )
- Monash University, Centre for Human Development
- Monash University, Centre for Industrial Design (1990s - )
- Monash University, Centre for Telecommunications and Information Engineering (CTIE) (1993 - )
- Monash University, Centre for Water Studies (1976 - )
- Monash University, College of Art and Design
- Monash University, Dairy Process Engineering Centre (1970s - )
- Monash University, Department of Chemical Engineering (1961 - )
- Monash University, Department of Chemistry (? - c. 2001)
- Monash University, Department of Civil Engineering (1961? - )
- Monash University, Department of Computer Systems Engineering
- Monash University, Department of Digital Systems (1996 - 1998)
- Monash University, Department of Geography and Environmental Science, Graduate School of Environmental Science (1972 - )
- Monash University, Department of Materials Engineering (1960s - c. 2001)
- Monash University, Department of Mechanical Engineering
- Monash University, Department of Medicinal Chemistry
- Monash University, Department of Microbiology
- Monash University, Department of Physics ( - c. 2001)
- Monash University, Department of Physiology (1962 - )
- Monash University, Department of Psychology
- Monash University, Department of Robotics and Digital Technology (1982 - 1996)
- Monash University, Faculty of Arts (1961 - )
- Monash University, Faculty of Computing and Information Technology
- Monash University, Faculty of Engineering (1961? - )
- Monash University, Faculty of Information Technology
- Monash University, Faculty of Medicine (1962 - c. 2001)
- Monash University, Faculty of Medicine, Nursing and Health Sciences (c. 2001 - )
- Monash University, Faculty of Science (1960s - )
- Monash University, Gippsland School of Computing and Information Technology
- Monash University, Gippsland School of Engineering (c. 1945 - 2003)
- Monash University, Monash Institute of Medical Research (MIMR) (2005 - )
- Monash University, Peninsula School of Computing and Information Technology
- Monash University, School of Applied Sciences (1990 - 2002)
- Monash University, School of Applied Sciences and Engineering (2003 - )
- Monash University, School of Business Systems
- Monash University, School of Chemistry (c. 2001 - )
- Monash University, School of Computer Science and Software Engineering (Caulfield) (1998 - )
- Monash University, School of Geography and Environmental Science
- Monash University, School of Historical Studies
- Monash University, School of Information Management and Systems
- Monash University, School of Physics and Materials Engineering (c. 2001 - )
- Monash University, Victorian College of Pharmacy (1881 - )
- Monash Universuty, Monash Institute of Reproduction and Development (1991 - 2005)
- Monier Industries Limited (c. 1935 - 1940s)
- Monier Limited
- Monier Research and Development Pty Ltd
- Monier State Pipe and Reinforced Concrete Works (1915 - c. 1935)
- Monsanto Australia Limited
- Monsanto Southern Cross (1928 - 1941)
- Monsanto Vic
- Morwell Power Station (1958 - )
- Motor Radiators Pty Ltd
- Moulded Products (1931 - 1967)
- Mount Bischoff Tin Mining Company (1873 - )
- Mount Coolon Gold Mines N.L. (1914 - 1939)
- Mount Isa Mines Limited (MIM) (1924 - 1970)
- Mount Isa School of the Air (c. 1964 - )
- Mount Lyell Mining and Railway Company Ltd (1893 - 1960s)
- Mount Newman Mining Co Pty Ltd (c. 1987 - 1992)
- Mount Stromlo and Siding Spring Observatories (c. 1967 - ), Australian National University
- Mount Stromlo Observatory - see Mount Stromlo and Siding Spring Observatories (c. 1967 - ), Australian National University
- Mount Stromlo Observatory (1957 - c. 1967), Australian National University
- Mount Tom Price Mine (1966 - )
- Mount Tom Price Power Station
- Movement Against Uranium Mining (c. 1976 - )
- Multicultural Mental Health Australia (MMHA)
- Munitions Supply Board (1921 - 1939), Commonwealth of Australia
- Munitions Supply Laboratories (MSL) (1922 - 1948), Commonwealth of Australia
- Munitions Supply Laboratories (MSL), Optics Section
- Murdoch University (1973 - )
- Muresk Agricultural College (1926 - 1985)
- Murray Committee (1958)
- Murray-Darling Basin Commission (1988 - ), Commonwealth of Australia
- Museum of Applied Arts and Sciences (c. 1945 - ), State of New South Wales
- Museum of Victoria (1983 - 1998)
- Museum Victoria (1998 - )
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