Interim Auditor General John Wiersema's report said from January 2010 through last April, more than 1 million visas seeking temporary residence and 300,000 seeking permanent residence were processed by Canada Border Services Agency workers along with staff of Immigration Canada.
Wiersma criticized the process as being inefficient and at times dangerous with regard to people with diseases, Postmedia News reported.
"We've been reporting some of these problems with visas for 20 years, and I find it disturbing that fundamental weaknesses still exist," his report said.
For some 50 years, Canada has denied visas to applicants with syphilis and tuberculosis although the auditor's report said there are now 56 diseases that require national surveillance.
Among his other criticisms is that there isn't sufficient security data-sharing for border agents from the Royal Canadian Mounted Police and the Canadian Security and Intelligence Service.
Wiersma said visa screeners rely on three federal manuals to determine eligibility for a visa, but two of them haven't been updated for years, Postmedia reported.