Admiral Oleg Yerofeyev said the craft, detected Wednesday eight kilometers off the entrance to Kola Bay, left only after being given several warnings.
But U.S. officials, who asked not to be identified, said no U.S. submarine had ventured within eight kilometers of the bay's entrance Wednesday.
The giant top-secret naval base at Severomorsk, home to the Northern Fleet, is only 30 kilometers downstream.
Foreign Ministry press chief Grigory Karasin confirmed that a submarine from an unidentified foreign power had been forced to leave Russian territorial waters Wednesday.
He told a news briefing that the craft was located in almost exactly the same spot where the U.S. nuclear submarine Baton Rouge crashed into a Russian nuclear submarine in February 1992.
Interfax said it was the third time in two years that a U.S. submarine had been found in Russian territorial waters -- an event that would have sparked a major crisis before perestroika.
Yerofeyev said such incidents "undermine the foundations of peaceful initiatives taken by the two countries," Interfax reported.
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