Auditor General Sylvain Ricard, who reports directly to parliament, said a probe showed the approach taken by the Canadian Border Services Agency (CBSA) "had not led to the timely removal of foreign nationals" from Canada, with about 50,000 cases still outstanding.
Besides data and case management issues, Ricard blamed inadequate information sharing and a lengthy appeals process.
"About 50,000 enforceable cases had continued to accumulate ... in two-thirds of these cases, the agency did not know the whereabouts of the individuals," he said in a report.
Public Safety Minister Bill Blair, who has overall responsibility for law enforcement, acknowledged shortfalls in the CBSA's performance.
"The CBSA will take specific measures to address concerns raised and it has already taken steps to better deliver on its mandate in relation to removals," he said in a statement.
Deportation orders are served against failed asylum claimants, people who overstay their visas and those with criminal records.