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Francis had told Russian youths in unscripted remarks following a speech on Friday to remember that they are the heirs of past tsars such as Peter I and Catherine II.
The two monarchs expanded Russia's empire in the 17th and 18th centuries, including conquering parts of Ukraine, and President Vladimir Putin has referred to their legacies in justifying his invasion and annexation of territory last year.
"The pope intended to encourage young people to preserve and promote all that is positive in the great Russian cultural and spiritual heritage, and certainly not to exalt imperialist logic and government personalities, (which he) mentioned to indicate some historical periods of reference," Vatican spokesman Matteo Bruni said in a statement.
Kyiv called the remarks "deeply regrettable".
The Kremlin, meanwhile, described the pope's comments as very gratifying, saying that the Russian state had a rich legacy and that it was good that the Pope knew Russian history.