Foreign Office official Sian MacLeod told the Russian deputy ambassador Alexander Kramarenko yesterday that she "could not be expected to comment upon reports of private conversations", and instead discussed the volatile situation in Ukraine.
The Prince's comment that "Putin is doing just about the same as Hitler" was made to 78-year-old Marienne Ferguson during a visit to Canada with the Duchess of Cornwall.
It was thought to be a reference to Russia's annexation of Crimea and the ongoing instability in Ukraine.
Ms Ferguson, a volunteer at the Museum of Immigration in Halifax, Nova Scotia, said she had told Prince Charles how her Jewish family fled the Nazis when they invaded the free city of Danzig at the outset of the Second World War, adding that he responded with the comments.
A statement issued by the Russian embassy in London denounced the comment as "outrageous".
"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," said the statement.
"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."
In a press conference, Russian Foreign Ministry spokesman Alexander Lukashevich said that Moscow "noted media reports quoting Prince Charles's statement, which he reportedly made during a private conversation on a trip to Canada".
He added: "If these words indeed were said, then they don't befit a future British monarch."