No, the government only sets drug prices. AFAIK private pharmacies buy and sell drugs at set prices and add stocking\service fee to sustain their business operations.
In almost all of the systems, medication is not covered unless you're a child, extremely poor, or very old.
In practice about 30% of all healthcare expenditure in Canada comes from private sources, since things like medication, dental care, vision care, and a whole myriad of other critical segments of healthcare are not covered by any government health plan.