Foreign Affairs Minister John Baird told the Commons Thursday the appointment of Mugabe as an international tourism ambassador was what led to the withdrawal.
The UN body, however, dismissed that reasoning, pointing out that it doesn't actually have an ambassadorial program.
The UNWTO said it gave an Open Letter on Travel and Tourism to the presidents of Zimbabwe and Zambia on May 29, in recognition of a tripartite agreement with both countries on the hosting of the 20th Session of the UN General Assembly in Victoria Falls, which straddles the borders of both countries.
The agency added that the same letter had been given to leaders of other countries around the world.
"The receiving of the Open Letter implies no legal commitment or official title attribution to the country or the recipient," the agency said in a statement.
But the mere recognition of Mugabe at a UN event was enough for Baird, who called it the "last straw" for Canada's participation in the UNWTO, the minister's spokesman said.
"After (minister Baird) heard that (Mugabe) was honoured at an event, after he was invited to join this global leaders group, he signed the Order in Council almost immediately," said Joseph Lavoie.
Canada had already signalled a year ago, by giving formal notice, that it intended to withdraw from the UNWTO. But an Order in Council is required to formalize any such notice period.
"They were legitimizing him by enlisting Mugabe to promote tourism," Lavoie said.
"In our view that makes him a small 'a' ambassador."
Mugabe is currently under a United States and European Union travel ban because of human rights abuses in his own country.
He has been in power for more than three decades and has been blamed for his country's economic ruin, resulting in food and fuel shortages, rampant inflation, high poverty and unemployment.