The banned cult was responsible for a deadly sarin nerve gas attack on the Tokyo subway in 1995, which killed 13 people and injured 5,000.
Ten people were detained in the St Petersburg raids, Itar-Tass news agency says. Forty-four Russians expelled from Montenegro are also being investigated.
Aum leader Shoko Asahara and 12 other cultists got death sentences in Japan.
The Russian raids targeted the homes and places of worship of suspected Aum cultists.
Russian prosecutors say the cult has been pressurising people for donations. They suspect it has up to 30,000 followers in Russia.
Aum Shinrikyo began as a spiritual group mixing Hindu and Buddhist beliefs but became a paranoid doomsday cult obsessed with Armageddon.
Some 189 Aum cultists have been put on trial in Japan. Their leader Shoko Asahara was sentenced to death in 2004 and remains on death row.
Russian police have raided 25 premises in Moscow and St Petersburg linked to the Japanese Aum Shinrikyo cult.