CN Rail owned most of the tracks in eastern Canada.

One year before the Crown corporation was privatized...
House of Commons Debates, Ottawa    February 7, 1994.

Mr. Alex Shepherd (Durham)
     "Mr. Speaker, those of us who are proud Canadians are offended that CP Rail has decided to change its company logo into what in effect looks like the Canadian flag becoming or being subsumed into the American flag,
     It is not just Canadians who are offended by this logo. This logo has also been challenged in the United States for defaming the American flag. Regardless of CP's rights as a private company to choose any logo it wants, Canadians should have a voice in this matter. CP Rail is a company that Canadian taxpayers have helped to establish through subsidies, outright gifts of land and other means.
     I note that most of the tracks in eastern Canada are owned by CN and more precisely the taxpayers of Canada. Currently CN, which displays the Canadian flag on its trains, and CP are in negotiation for consolidation of rail services in eastern Canada. I would like to bring this matter to the attention of the House so that we can convey our desire to have the Canadian flag and not the offensive logo of CP Rail flying over taxpayers' property in eastern Canada."

The CPR logo from 1993 until 1996.

After the Crown corporation was sold off the CN Tower became "Canada's National Tower."