The raid on the controversial US-based Church comes after Russia's Supreme Court in April issued a ruling banning Jehovah's Witnesses and seizing their property, with the justice ministry calling the Christian evangelical movement an "extremist organisation."
The FSB security service raided the Church of Scientology's buildings and also the homes of church members, a spokeswoman told Rossiya 24 television.
No one at the Church of Scientology was immediately available for comment.
The FSB said in a statement released to Russian news agencies that the probe was initially launched into the Church's earnings from selling educational materials to new recruits.
In 2016 the Russian Supreme Court ordered the closure of the Moscow branch of the Church of Scientology in a case launched by the justice ministry.
The justice ministry has ruled that a number of the Church's publications are extremist and calls the organisation a sect.
The Church of Scientology was founded in the United States in 1954 by science-fiction writer L. Ron Hubbard and was accorded the status of a religion there in 1993.
The European Court of Human Rights has twice ruled in favour of the church, saying that Russia violated its rights by refusing to register its churches in various regions.
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