The national headquarters is composed of several functional directorates reporting to the commander: Or to the surgeon general: Health Services Secretariat includes public affairs, legal advisor, policy and records, and privacy that advise both the commander and surgeon-general.

Canadian Forces Health Services Training Centre (CFHSTC) Home station at CFB Borden, Ontario The School of Operational Medicine (SOM) in Toronto, Ontario forms a part of the Canadian Forces Environmental Medicine Establishment.

In turn the Canadian Forces Environmental Medicine Establishment is the military component of the Defence Research and Development Canada.

The School of Operational Medicine (SOM) conducts all Flight Surgeon training.

The training covers diverse topics including life support equipment and human factors, search and evasion as well as disorientation and night vision.