A border guard became suspicious of the 17- and 18-year-old males during questioning on Sunday.
Under secondary questioning, border services officers found inconsistencies in answers from the teens and thought they might be what the agency calls "internal narcotics carriers".
Both were taken to hospital as a precaution.
Health officials decided the pellets were deteriorating and both teenagers needed emergency surgery to remove the drug, which is believed to be methamphetamine.
The CBSA says one traveller was carrying 229 pellets weighing more than half a kilogram, while the second male had 79 pellets in his system.
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