Deputy ambassador Alexander Kramarenko is heading to meet senior British diplomats at the Foreign Office to raise Moscow's displeasure at the comments made by Charles during a royal tour of Canada.
The remarks came during a tour of the Museum of Immigration in Halifax, Nova Scotia, where he and the Duchess of Cornwall paid tribute to Second World War veterans and their families.
Jewish museum volunteer Marienne Ferguson, 78, told the Prince how she and her family fled the Nazis during the war, and said that he responded: "Putin is doing just about the same as Hitler."
A statement issued by the embassy in London said: "The minister-counsellor of the embassy, Mr Alexander Kramarenko, will meet this afternoon the representatives of the FCO to discuss a range of bilateral issues.
"The outrageous remarks made by Prince Charles in Canada will be among the questions raised. The embassy asked the FCO for official clarifications on that yesterday."