The Investigative Committee (SK) posted a video on YouTube showing SK men in balaclavas breaking into a flat and seizing piles of foreign currency.
The SK - which operates like the FBI - said "conspiratorial meetings" had been held at a Moscow flat since June 2019.
In 2017 Russia's Supreme Court banned the Jehovah's Witnesses as "extremist".
According to the SK, the Moscow group "studied religious literature... propagandising Jehovah's Witnesses teachings". It said they "indoctrinated and recruited new members among the capital's residents and in other regions, to participate in the banned religious movement".
Dozens of the faith's followers are being prosecuted in Russia for practising their religion.
In July the UK government voiced concern about Russia's crackdown on Jehovah's Witnesses, saying the state had "criminalised the peaceful worship of 175,000 Russian citizens and contravened the right to religious freedom that is enshrined in the Russian constitution".
In December 2018 Russian President Vladimir Putin said he could not understand why followers of the religion were being persecuted.
The Russian Orthodox Church welcomed the ban in 2017. A senior Orthodox cleric, Metropolitan Hilarion, called the Jehovah's Witnesses a "totalitarian sect" on Russian TV.
He said: "It's hard to deny that these cultists will remain and continue their activity... but at least they'll stop openly claiming to be a Christian faith, in other words, in the market place of existing Christian confessions this product will no longer be on display.
"And I think that's all for the best. It'll save families, people's lives".
The Jehovah's Witnesses were founded in the US in the late 19th Century and stick to a very literal reading of the Bible, rejecting the interpretations of many Christian scholars and the Christian doctrine of the Trinity.
They believe that the final battle between good and evil will happen soon. They are also pacifists, carry out door-to-door preaching and oppose blood transfusions.