The arrest of Timur Ivanov, a long-time ally of Defence Minister Sergei Shoigu, is the most dramatic corruption case in Russia in recent years. It comes as spending on the military has ballooned amid its offensive on Ukraine.
Ivanov, 48, oversaw construction and procurement for the armed forces, and was linked to Russia's high-profile rebuilding of the Ukrainian city of Mariupol, occupied by Moscow's forces.
"The deputy defence minister of the Russian Federation was sent to a pre-trial detention centre," the press service for Moscow courthouses said in a statement on social media.
He faces up to 15 years in prison for bribe-taking "on a particularly large scale", it added.
Ivanov denies the charges, his lawyer told the state-run TASS news agency.
Several independent Russian media outlets have alleged that Ivanov and his family acquired vast wealth through kick-backs on contracts he agreed at the ministry.
- Lavish lifestyle -
In December 2022, Navalny's team said they had obtained thousands of leaked emails from Ivanov's wife, Svetlana Maniovich, that showed a lavish lifestyle well beyond what his official salary could cover.
They said she had spent hundreds of thousands of euros on luxury cars, jewellery, clothes, parties, and renting premium property and yachts in the south of France.
Some of the transactions were routed through third parties, including defence ministry contractors, they alleged.
The Kremlin said President Vladimir Putin was in "constant" contact with Shoigu but refused to comment directly on Ivanov's arrest.
"There will be an investigation," spokesman Dmitry Peskov said, cautioning against "speculation".
In court on Wednesday, Ivanov, 48, stood in a glass dock for defendants in military uniform.
The court said investigators believe he was part of a "criminal conspiracy" to take a "bribe on a particularly large scale in the form of property services, during the course of contracting and subcontracting work for the defence ministry."
It did not provide further details.
The judge sent him to pre-trial detention until at least June 23. He will be held at the notorious Lefortovo jail in Moscow, TASS reported.
- 'Shoigu's deputy' -
Campaigners, including Navalny, have long argued that corruption is endemic in Putin's Russia.
Arrests of high-profile government figures are rare, usually the result of political infighting, analysts say.
Activists say the vast sums being poured into the Ukraine offensive has given officials new opportunities to enrich themselves through secretive procurement deals.
Russian military bloggers, who have long criticised Shoigu's handling of the offensive, quickly linked Ivanov to the defence minister on social media.
In a post criticising Ivanov, Wagner-linked Telegram channel Grey Zone repeatedly referred to him as "Shoigu's Deputy".
"He, like Shoigu, comes from the family clan," it said.
Former Wagner boss Yevgeny Prigozhin had accused Shoigu and other defence ministry officials of corruption and incompetence before his mysterious death last year.
The defence ministry has not commented on Ivanov's arrest.
Just hours before investigators announced they had arrested Ivanov on Tuesday he had appeared in video footage published by the ministry in which Shoigu addressed top military brass about the state of the Ukraine offensive.
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