Jehovah Witness has 395 centres across Russian Federation.
Four former members of the Jehovah's Witnesses had told a Russia's Supreme Court how they were brainwashed by the church against receiving higher education or starting a family.
The Jehovah's Witnesses claim more than 170,000 adherents in Russian Federation.
The Russian Supreme Court ruled Thursday that the Jehovah's Witnesses, a Christian sect, are an "extremist" group and ordered their Russian property turned over to the government.
The report further stated that the Russia's justice ministry attorney Svetlana Borisova was quoted as saying that the Jehovah's Witnesses "pose a threat to the rights of the citizens, public order and public security".
"We fear that people will end up in jail", he said.
The ministry was investigating the Jehovah's Witnesses' Russian headquarters near St. Petersburg over the a year ago and claimed it discovered violations of a Russian law banning extremism.
It came hours after the justice ministry applied for an order to shut down the group's national headquarters near St Petersburg, news groups said.
The Justice Ministry began an investigation into the group's practices in February.
The US-based group has generated controversy for stances including its rejection of blood transfusions and opposition to military service, facing court proceedings in several countries. The Russian government cracked down on the group past year when it banned Jehovah's Witnesses literature they considered a violation of national security laws.
In January, the chairman of the group's branch in the town of Dzerzhinsk was fined for having distributed material that authorities deem extremist, local media reported.
Russian Federation blocked the Jehovah's Witnesses' worldwide website two years ago over alleged extremism, and the group's Bibles were banned last year.
The Organisation for Security and Co-operation in Europe (OSCE) was among the global bodies condemning a "state sponsored campaign of harassment and mistreatment of Jehovah's Witnesses" it said dated back to the 1990s in Russian Federation.