The court remanded Deputy Defence Minister Timur Ivanov in custody for two months and said according to the charges he had put himself in a position to benefit from hiring contractors for the ministry where he oversaw construction activities.
Ivanov was detained on Tuesday, according to a brief 22-word statement by Russia's investigative committee.
The statute that the investigators cited for his detention is for accepting bribes "on a particularly large scale".
He faces 15 years in jail if convicted.
The sudden arrest of an ally of Shoigu, who Putin tasked with fighting the war in Ukraine, triggered speculation about a battle within the elite and of a public crackdown on the corruption that has plagued Russia's post-Soviet armed forces.
The Kremlin said Putin had been informed, and added that Shoigu had also been told. Ivanov was present earlier on Tuesday at a meeting of top defence officials chaired by Shoigu.
Ivanov, who has served as deputy minister since 2016, was in charge of property management, housing, construction and mortgages at the defence ministry. The defence ministry has made no comment.
Russia's Kommersant newspaper said that Ivanov, 48, was arrested by the Federal Security Service (FSB), the successor to the Soviet-era KGB which Putin last month told to root out corruption in state defence procurement.
The Izvestia newspaper said others had also been detained, though there was no official confirmation of that. The newspaper said Ivanov's properties were being searched. State television gave the case full coverage.
"Let's just say the investigation did not start yesterday, the day before yesterday or even a month ago," an unidentified Russian law enforcement source told the TASS state news agency. FSB military counter-intelligence was involved, TASS said.
It was not immediately clear why such a senior official with a close association with Shoigu would be targeted.
Russian military bloggers have long accused top generals of corruption and incompetence, especially after the army's hurried withdrawal from parts of Ukraine after seriously over-extending itself during the first days of the invasion.
Ivanov, who could not be reached as he was in detention, has long been linked to the ostentatious opulence that has characterised some sections of the post-Soviet Russian elite, including luxurious real estate and flashy parties.
In 2022, Russia's Anti-Corruption Foundation, headed by the late Russian opposition leader Alexei Navalny, alleged that Ivanov and his family led a lavish lifestyle.
Forbes magazine listed Ivanov as one of the wealthiest men in Russia's security structures.
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