If convicted, Anatoly Serdyukov could face up to five years in prison. Serdyukov denies any wrongdoing, his lawyer Konstantin Rivkin told the Interfax news agency.
President Vladimir Putin fired Serdyukov a year ago over a corruption scandal, but most military experts believed his ouster reflected a behind-the-scenes power struggle.
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A close ally of Serdyukov's was charged last year with fraud, but Serdyukov had been spared until today, when Russia's main investigative agency charged him with negligence.
Investigative Committee spokesman Vladimir Markin said in a statement that Serdyukov had used railroad troops to build a road to an island in the southern Astrakhan region and conscripts from an aviation unit to do landscaping around a vacation home there.
"So instead of serving and being trained in military affairs, some soldiers were busy planting poplar trees," Markin said.
It was only during this year's investigation that the property was put on the Defense Ministry's books, the spokesman said.
Serdyukov had caused damages to the state of USD 1.7 million, Markin said, adding that the investigation was still under way and more charges could be filed.
A former furniture salesman, Serdyukov had entered public service as a tax official and quickly rose through the ranks to become head of the Russian tax service before being appointed defence minister in 2007.
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