Moscow said the comments were "not worthy of a future British monarch", while a senior Russian diplomat was heading for the Foreign Office in London to lodge a protest over the heir to the throne's remarks.
Charles, 65, made the apparently unguarded comment during a trip to a museum in Canada, in a private conversation with a Polish-born woman who had fled the Nazis as a child, the Daily Mail newspaper reported.
"If these words were really said, then undoubtedly they are not worthy of a future British monarch," foreign ministry spokesman Alexander Lukashevich said in Moscow.
The Russian embassy in London issued a separate statement saying deputy ambassador Alexander Kramarenko would raise the "outrageous remarks made by Prince Charles in Canada" in his meeting today.
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The Prince's office, Clarence House, declined to comment on the Russian reaction when contacted by AFP today.
But it said yesterday that Charles "would not seek to make a public political statement during a private conversation."
The comments by Charles were reported by the Daily Mail yesterday.
"I had finished showing him the exhibit and talked with him about my own family background and how I came to Canada," 78-year-old Marienne Ferguson told the paper.
Russia's Lukashevich slammed Western media for using Charles's reported words in what he said was a propaganda campaign against Russia.
"We consider it is unacceptable, disgusting and low that Western media are using members of the British royal family to unroll a propaganda campaign against Russia on a contentious international issue like the situation in Ukraine," he said.
Russia and Britain's positions "differ widely and that is obvious, we see that from the statements of British politicians," Lukashevich said.
"To discuss these topics, we have absolutely legal two-way channels and that does not call for pronouncing judgements in a broad public forum."