The incident, which was captured by a British passenger of Air Canada's flight from Montreal to Heathrow in Jul 2010, violates international standards, which require airport check-in staff to see the faces of passengers who board their flights.
The video, which was posted under the title 'A major Canadian airline risks your safety, pandering to Muslim sensibilities', with titles and soundtrack, drew thousands of hits and racist comments.
"I have instructed my department to immediately look into this matter and report back," said Transport Minister, John Baird on Sunday, Aug 1.
He also added, "if our current security policies in this area are deemed to be lacking, our government will take the necessary steps to protect the safety and security of the travelling public.''
Calling the incident "deeply disturbing'', the minister said such neglect poses a serious threat to the security of the air traveling public.