The dispensers have been spitting back the new currency, which is made with a polymer material to foil counterfeiters but is unpalatable to many vending machines.
Officials at GO Transit in Toronto and Translink in Edmonton, Alberta, told CBC News the upgrades were already under way.
Bank of Canada told CBC News such glitches can occur when new bills are put into circulation.
"It's a natural thing when we change series," said senior bank analyst Julie Girard. "Even when we've changed from one paper series to the next before polymer was introduced we still had to upgrade the machines."
CBC said the transition to polymer bills began this year with new $100 and $50 notes. The widely used paper $5 and $10 bills will convert to polymer next year.