Cadet Vadim Osipov was ordered to be held in custody until June 9 as investigations continue, the press office for the military court said, without giving more details about the case.
The announcement of the arrest comes in the wake of a deadly bomb attack on the city's metro system on April 3 that killed 14 people.
Officials made no link between Osipov's detention and the metro bombing.
Authorities have blamed that attack on 22-year-old Akbarjon Djalilov, thought to be a Russian national born in Central Asian Kyrgzstan, who died in the blast.
Eight people -- all from mainly Muslim Central Asia -- have been detained in Moscow and Saint Petersburg over alleged involvement in the attack.
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