Anatoly Serdyukov lost his job a year ago over a corruption scandal. Some of his close associates have faced criminal charges, but the Kremlin has faced repeated questions about why the ex-minister himself remained immune from prosecution.
Thursday's move by Russia's main investigative agency could be an attempt to fend off such public criticism and demonstrate the government's readiness to investigate high-level graft.
Serdyukov, who has been summoned for questioning on Tuesday, is charged with negligence and could face up to five years in prison if convicted. He denies any wrongdoing.
Sergei Zheleznyak, deputy chief of the main Kremlin party, United Russia, was quoted by the state RIA Novosti news agency as saying that "the tough action against officials who discredit the government will become a clear signal for all civil servants."
Gleb Pavlovsky, a one-time Kremlin political consultant, said that filing charges against Serdyukov would allow the Kremlin to deflect the opposition criticism. "It's a maneuver that takes into account public opinion and political risks," he said, according to Interfax.
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 air force unit to do landscaping around a vacation home there.
Although the vacation home officially belonged to the Defense Ministry, it was only during this year's investigation that the property was put on the ministry's books, the spokesman said.
Serdyukov caused damages to the state of 56 million rubles ($1.7 million), Markin said, adding that the investigation was still under way and more charges could be filed.
A former furniture salesman, Serdyukov entered public service as a tax official and quickly rose through the ranks to become head of the Russian tax service before being appointed defense minister in 2007.
While the Kremlin has presented Serdyukov's ouster as part of a crusade against graft, many military experts said it reflected a behind-the-scenes power struggle over a military modernization program worth billions of dollars. During his tenure, Serdyukov oversaw a radical military reform that drastically cut the number of officers and demanded higher quality and cheaper prices from defense industries.
The investigators have alreday targeted some of his associates, including Yevgeniya Vasilyeva, the former head of the ministry's property department who widespread media reports say was having an affair with Serdyukov.
She was charged with fraud related to the sale of military assets. The Investigative Committee said in October that it had confiscated 57,000 diamonds, rubies and emeralds and 19 kilograms (42 pounds) of gold and platinum jewelry from her.
In recent weeks, Vasilyeva, who has remained under house arrest in her posh apartment in downtown Moscow, has issued a series of statements insisting on her innocence.
Yevgeny Minchenko, a political consultant close to the Kremlin, said that Vasilyeva's defiance could have helped trigger charges against Serdyukov. "Vasilyeva is a strong irritant for public opinion," Minchenko told Interfax.