Day-to-day administration of the NCE centres and networks is provided by the Networks of Centres of Excellence Secretariat. The Secretariat runs periodic national competitive processes through which successful applicants are chosen on the advice of a number of panels and boards. In the case of the Networks of Centres of Excellence program, applications are reviewed by an expert panel, a Selection Committee and a Steering Committee. Applications for the CECR and BL-NCE programs are reviewed by an expert panel, the Private Sector Advisory Board and the Steering Committee.
The NCE programs are overseen by a tri-agency NCE Steering Committee made up of the Deputy Minister of Industry and Health (or delegate), the Presidents of the three granting agencies and the President of the Canadian Foundation for Innovation (CFI) (as an observer).