In 1992, the Federation began a multi-year restructuring process that resulted in significant changes in the way the organization was governed. The organization hired its first part-time Chief Executive Officer in 1996 and was officially incorporated in 1999. Under its newly revised Constitution and By-laws, the Board of Directors was comprised of three representatives from each of the 12 provincial and territorial licensing authorities.
The Board of Directors met once a year. The affairs of the organization were governed by a six-person Executive Committee that met four to six times a year. Registrars and Deputy / Associate / Assistant Registrars could be elected to the Executive Committee. The President was elected by the Members for a one-year term , usually after serving as a member-at-large on the Executive Committee for three years and as President-elect for one year.
The annual meeting of the Board of Directors also included observers from the medical organizations that were officially recognized as associate members, i.e.: Association of Canadian Medical Colleges, Canadian Association of Internes and Residents, Canadian Federation of Medical Students, Canadian Medical Association, College of Family Physicians of Canada, Fédération des médecins résidents du Québec, Federation of State Medical Boards (U.S.), the Medical Council of Canada and the Royal College of Physicians and Surgeons of Canada.
Some of the issues that were considered by the Federation during that decade are:
- the autonomy of licensing authorities
- Agreement on Internal Trade
- Monitoring and Enhancement of Physician Performance or MEPP (Aylmer Conferences I-IV)
- the transition to the requirement for two years of postgraduate medical education for family physicians
- being a founding member of the Canadian Medical Forum, the International Association of Medical Licensing Authorities and the Canadian Network of National Associations of Regulators met for the first time internationally meeting.
- alternative therapies
- Medical Identification Number for Canada
- telemedicine
- evaluation of international medical graduates
- the new Immigration Act
- reproductive and genetic technologies