In 2004, Transport Canada introduced non-passenger screening to enhance both airport and civil aviation security.

These responsibilities include: As of 2003 the Office of Boating Safety and the Navigable Waters Protection Program were transferred back to Transport Canada.

This includes providing services that are mandated by acts and regulations such as certification for Canadian seafarers and related professionals.

In 2005, the United States was discussing a similar delegation of the FAA's air traffic services to an "arm's-length" government corporation.

Transport Canada also collects data on all accidents and incidents, no matter how minor, using the Civil Aviation Daily Occurrence Reporting System (CADORS).

[12] Transport Canada continues to be responsible for licensing pilots and other aviation specialists (such as dispatchers and mechanics) as well as registering and inspecting aircraft.

[13] In spring 2017 CATSA and the Canada Border Services Agency began their roll-out "as part of a broader effort to modernize and streamline clearance procedures at Canadian airports" of the self-service border clearance kiosks programme, under which Canadian travellers are subject to facial recognition technology upon re-entry to the country.

It was expected that as a cost-cutting measure the programme was to reduce the number of civilian interactions with civil servants.

In September 2009, the CBC's Fifth Estate produced a report "Riding on Risk", which detailed alleged mismanagement and cover-ups in Transport Canada.

[20] Transport Canada's move to Safety Management Systems (SMS) in its regulation of civil aviation has been criticised.

Whistleblower Hugh Danford, a former inspector at Transport Canada, went on record[21] criticizing this approach, indicating that it would increase risk to the flying public.

[24] Several Transport Canada senior executives, including Assistant Deputy Minister, Safety and Security, Marc Grégoire, were sued in 2008 for reprisals against another whistleblower, Ian Bron.

[27] The Canadian Association of Journalists[28] nominated Transport Canada for its Secrecy Award for a second time in 2008, indicating that a bill to amend the Aeronautics Act will cause "a veil of secrecy [to] fall over all information reported by airlines about performance, safety violations, aviation safety problems and their resolution.

"[29] In September 2009, Transport Canada was alleged to have fraudulently charged expenses to the non-existent Mackenzie Valley Pipeline project.