The move comes a week after the United States government announced it would also skip the regular meeting of countries who are part of the WHO Framework Convention on Tobacco Control. Washington has not yet ratified the treaty.
Canada is one of the founders of the tobacco convention, but Eve Adams, the parliamentary secretary to Health Minister Rona Ambrose, said the government would boycott the event on principle.
The federal government has been vocal in its opposition to Russian aggression in Ukraine, particularly the annexation of the Crimean region.
"I am pleased to inform this House that Canada will boycott the next meeting in Moscow," Adams said during question period.
"We stand with the people of Ukraine and we will offer no legitimacy to the Putin regime's actions in Ukraine when it comes to these farcical conferences that they try to pull out some legitimacy on."
Part of the conference includes a progress report on how countries are complying with the treaty, and what sort of legal challenges they are facing from the tobacco industry.
The topic of how to regulate the use of e-cigarettes is also on the agenda.