Vladimir Puchkov was flying Friday to the Siberian city of Novosibirsk aboard a Yak-42, a mid-range passenger jet with three rear-mounted engines.
The pilots were able to land the jet safely at Novosibirsk's Tolmachevo Airport, ministry spokeswoman told the Interfax news agency. There was no immediate indication of what caused the engine failure.
A day earlier, Puchkov was quoted as denying speculation that the world will come to an end on Dec. 21, as many people believe the Mayan calendar predicts.
He told the newspaper Rossiiskaya Gazeta not to expect "serious cataclysms" on that day.