Anatoly Serdyukov has been replaced with a former emergencies minister and loyal ally to Vladimir Putin, Sergei Shoigu.
Russia’s top investigative agency is investigating the sale of ministry assets at prices below market value.
Vladimir Putin said he had removed Anatoly Serdyukov to create “conditions for an objective investigation”.
Last month, Russian investigators raided the offices of a state-controlled military contractor and began investigating the company on suspicion that it had sold assets to commercial firms at a loss of nearly 3 billion roubles ($100 million).
Oboronservice’s activities include servicing military aircraft and arms and constructing military facilities.
Anatoly Serdyukov was a furniture store executive and head of the Russian tax service before being appointed defense minister in 2007.
In the six years that Anatoly Serdyukov had been minister he had tried to reform Russia’s outdated armed forces by cutting costs and personnel and by boosting efficiency.
But he had made enemies along the way, and fell out with his own father-in-law, the former deputy prime minister Viktor Zubkov.
Anatoly Serdyukov may now face questioning as part of the fraud investigation.
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