Safonov, 48, "was transferred to a different office," the Kremlin said in a statement on its web site.
Medvedev appointed State Duma Deputy Vyacheslav Shport as the acting Khabarovsk governor and has nominated him for a full term. The Khabarovsk regional legislature is to consider his candidacy Wednesday.
Safonov was appointed envoy to the Far East Federal District in 2007 by then-President Vladimir Putin.
"Decriminalizing the region will be one of your priority tasks," Putin told Safonov at the time of his appointment.
Like Putin, Safonov served in the Soviet intelligence services in the 1980s. He was a deputy interior minister before his appointment as envoy to the Far East. Citing an unidentified Kremlin source, Vedomosti reported Monday that Safonov was removed from his post because he was too quick to use law enforcement officers to deal with regional officials, while the "situation there demanded finer tools."
Ishayev, one of the country's longest-serving governors, had headed the Khabarovsk region since 1991.
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