The rollout forms part of wider CSIRO efforts to install enterprise-wide systems across its 21 divisions. The strategy, dubbed 'OneCSIRO', aims to unify and streamline management of the organisation.
Fujitsu said the project would be the first in Australia to be based on its FlexFrame for mySAP Business Suite.
The services giant said the contract win would create 30 new jobs, and expand its SAP practice in Canberra.
As part of the contract, Fujitsu will also manage the infrastructure to support the mySAP environment, including security, hosting and service desk.