Three people could be seen being led by officers down the gangway shortly after the arrival in Harbour Grace of the trawler Newfoundland Lynx.
A spokeswoman for the agency said last week that the stowaways would be processed according to Canadian law.
She said officers would interview the stowaways and what happens next would depend on the documentation provided.
It hasn't been revealed where the stowaways are from, but reports indicate they may be from Africa.
The stowaways were apparently discovered after the fishing boat left Iceland earlier this month.