Tax police and other security services spent 16 hours confiscating materials from the Scientologists' Moscow center on Thursday, and they returned today to question the leaders, the group said.
Authorities said they were investigating possible tax evasion and other financial irregularities.
Russian authorities have moved against a number of religious organizations following the passage of a 1997 law that placed widespread restrictions on "nontraditional" faiths.
The dominant Russian Orthodox Church strongly supports the law and often speaks out against religious groups that have been arriving in Russia since the Soviet breakup in 1991.
The Scientologists said the investigation against them was politically motivated.
"Cruelty was in the air during this visit (by the tax police), which has reminded us that Russia has not yet acquired the right of freedom -- freedom to think and act in accordance with the convictions of conscience," Alexei Danchenkov, a Scientologist spokesman, said in a statement.
Some 200 students a week attend classes at the Scientologists' center in Moscow, said Danchenkov.
Human rights groups say the religious law is reminiscent of anti-religion drives during the Soviet era, when the Communists decreed an official policy of atheism and many religious groups had to operate underground.
Other current religious cases include: