W previously explained the process for reporting hazards and concerns in Reporting UAV Issues in Canada – CAIRS

As of March 31 2016 the process has changed as noted on the Transport Canada website:

IMPORTANT NOTICE: Please note that as of March 31, 2016, the Civil Aviation Issues Reporting System (CAIRS) database will be decommissioned.

We have streamlined our service delivery processes in order to improve efficiencies, and as a result of these changes, the aviation community and the public will report issues or concerns through the Civil Aviation Communications Centre, which currently provides a central point of contact for email and phone requests about the Program. Please contact us by the methods outlined below:

Requests to:services@tc.gc.ca or by Facsimile 613-957-4208
Questions to: 1-800-305-2059

In an effort to maintain confidentiality, steps have been taken by the communication centre to handle confidential enquiries, but incoming submission must be clearly marked as confidential in the title and body of the submission.

Source: https://www.tc.gc.ca/eng/civilaviation/opssvs/secretariat-cairs-menu-209.htm