Police reportedly forced Roman Dobrokhotov into a car April 29 after he tried to enter the church to pray for Russia's deliverance from Putin, who has led Russia as president and prime minister for the last 12 years and is due to begin another presidential term in May.
Dobrokhotov said he was beaten by several men after he was released from custody.
The case comes amid the ongoing prosecution by Russian authorities of three members of the female band Pussy Riot, who were arrested after staging a performance against Putin inside the cathedral in February.
WATCH: Orthodox Christian believers and police scuffled with a group of opposition activists who were trying to enter Russia's largest Orthodox cathedral on April 29. The activists had planned to stage a public prayer for Russia to be saved from Prime Minister and President-elect Vladimir Putin. One opposition activist was reportedly detained by the police. RFE/RL's Russian Service