The CSIRO will reduce its number of National Research Flagships from 11 to nine, with the Future Manufacturing Flagship to remain, as the organisation restructures.
The two divisions to be cut on July 1 are Climate Adaptation and Preventative Health, Fairfax reports.
CEO Dr Megan Clark, who will leave the organisation in December, said, "It is time to collapse the matrix" when discussing a review of the organisation’s structure.
The National Research Flagships program began in 2003 with three Flagships.