AMI achieves its missions through the work of its 5 departments: Drug Resistance and Diagnostics, Drug Evaluation, Clinical Studies and Surveillance, Vector Surveillance and Control, and Arbovirology (see AMI Structure). There is naturally considerable interaction between department heads in meeting these objectives. Each department head has either a military or civilian appointment in the Department of Defence. Some of the department heads also have adjunct academic appointments with the Faculty of Health Sciences at the University of Queensland.
Departmental activities are supported by the Administration section, the Quality Management section, and various committees, such as the Institutional Biosafety, Occupational Health and Safety, and Animal Experimentation Ethics committees. Studies involving human volunteers are reviewed by the Australian Defence Human Research and Ethics Committee.