Initial developmental funding for the NCIS in 1998/99 was provided by Monash University, the Victorian Department of Justice, the Commonwealth Department of Health and Aged Care; the Federal Office of Road Safety; and the National Occupational Health and Safety Commission.

Between 2000 and 2003, during further development and consolidation, funding was provided by each State/Territory Justice Department and the Commonwealth agencies of the Department of Health and Ageing; the National Occupational Health and Safety Commission; the Australian Transport Safety Bureau; the Australian Institute of Criminology, and the Department of Treasury.

Funding by these government agencies was provided on the condition that after July 2003, a user pays system be adopted to finance the operations of the NCIS. Accordingly a user pays system for third party users was implemented in 2003/04, however it soon became clear that income from this initiative was unlikely to sustain NCIS operations in full. Further government funding was subsequently sought and approved.

The NCIS is currently funded through a joint Commonwealth and State initiative by the following agencies:

• The Justice Departments of each State/Territory
• The Commonwealth Department of Health and Ageing
• The Australian Institute of Criminology
• The Office of the Australian Safety and Compensation Council (known previously known as the National Occupational Health and Safety Commission)
• The Australian Competition and Consumer Commission

The NCIS has also received support from a range of agencies including the Australian Bureau of Statistics; Flinders University Research Centre for Injury Studies; The Victorian Institute of Forensic Medicine; Monash University Accident Research Centre; and the Monash University Department of Epidemiology and Preventive Medicine.