[5] On February 20, 2006, the editor-in-chief, John Hoey, was fired over an editorial independence dispute with the then owners of the journal, CMA Media.

The journal sent 13 women to buy the emergency contraceptive levonorgestrel (Plan B) over-the-counter in pharmacies across Canada and reported their experiences.

The pharmacists asked them for personal data, including the women's names, addresses, dates of last menstrual period, when they had unprotected sex, customary method of birth control, and reason for dispensing the medication.

[10] On February 29, 2016, a similar controversy re-surfaced as the Canadian Medical Association disbanded the CMAJ's Journal Oversight Committee and dismissed editor-in-chief John Fletcher.

The CMA cited a falling impact factor and a decline in research submissions as reasons for the change, but these claims are disputed.

Diane Kelsall, a long-time CMAJ deputy editor, became interim editor-in-chief while the organization searched for a permanent replacement.