A statement from the CSIRO said the partnership was worth $20 million and comprised an investment in the agency's metal membrane technology, which allows ammonia to be used as a carrier material for hydrogen storage and transport.
In August, the CSIRO announced that it had successfully refuelled two fuel cell vehicles that use ultra-high purity hydrogen which was produced in Queensland using the organisation's membrane technology.
Two cars, the Toyota Mirai and Hyundai Nexo, were tested using this method.
The CSIRO will work with Fortescue to identify, develop and commercialise technologies to support the creation of an Australian hydrogen industry and future global uptake.
The agreement includes commercialisation arrangements for the membrane technology, with a subsequent five-year investment in hydrogen R&D.
CSIRO executive director Dr Larry Marshall said the agency had a long history of collaborating with industry, "not just helping existing industries reinvent themselves through global disruption, but actually inventing entirely new industries like hydrogen where Australia can take the lead".
“Today we’re seeing a ‘market pull’ from companies like Fortescue to reinvent themselves through deep science-driven innovation and follow the global market shift towards a low-emissions energy future, and in so doing create a whole new export market for our vast clean energy resources.
“This partnership is great news for Australia, not just through new industry creation and the jobs that will flow from it, but in contributing to a different energy future that is secure, affordable, and sustainable.”