The Investigative Committee formalized the charges against Serdyukov on November 28.
He is accused of using servicemen and government funds to build a road to the vacation home and do landscaping work on the property.
The holiday facility reportedly belonged at the time to Serdyukov's son-in-law.
The measures authorized by the former defense minister are estimated to have caused damage of $1.6 million in public funds.
Serdyukov faces up to three months in prison if convicted of the charge.
Serdyukov headed Russia's tax service before being appointed defense minister in 2007.
He was fired a year ago over a corruption scandal.
Serdyukov is the son-of-law of former Prime Minister Viktor Zubkov, a close ally of President Vladimir Putin.