The Networks of Centres of Excellence is jointly administered by Canada's three research granting agencies: Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council (NSERC) and the Social Sciences and Humanities Research Council (SSHRC). This is done in partnership with Innovation, Science and Economic Development Canada (ISED) and Health Canada.
A Steering Committee made up of the presidents of the three granting agencies and the deputy ministers of both ISED and Health Canada oversees the Networks of Centres of Excellence. The President of the Canada Foundation for Innovation (CFI) sits on the committee as an observer.
The Steering Committee is assisted by the NCE Management Committee, which is made up of a vice-president from each of the three granting agencies, the assistant deputy ministers of ISED and Health Canada, as well as the associate vice-president of the NCE.
Day-to-day administration of the NCE centres and networks is provided by the NCE Secretariat. The Secretariat runs periodic national competitive processes through which successful applicants are chosen on the advice of a number of expert panels and selection committees.