A wtiness, Natalia Koretskaya from St. Petersburg had told the court she had been a member of that organisation from 1995 to 2009 and had realised over this period that the organisation's members "were living under full and total control of the [Jehovah's Witnesses] Administrative Centre".
The group, which has 395 centres across Russian Federation, has vowed to appeal the decision.
Russian authorities have put several Jehovah's Witness publications on a list of banned extremist literature.
Russia's Supreme Court banned Jehovah's Witnesses on Thursday, calling the Christian sect an extremist group.
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.
Justice Ministry attorney Svetlana Borisova said in court Thursday that the Witnesses " pose a threat to the rights of the citizens, public order and public security", the Interfax news agency reported. Reacting, it said it wold appeal the decision. They also reject military service and blood transfusions.
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The religious organisation has expanded around the world and has about eight million active followers.
Its members are known for preaching on doorsteps, where they offer religious literature and attempt to convert people.
The government has cracked down on the group in recent years, imposing fines on congregations and occasionally arresting leaders perceived to be stoking anti-government sentiment.
In 2010, the European Court of Human Rights ruled that a previous Russian judgment against the organization was "unlawful".
In 2004, Moscow dissolved a branch of the Jehovah's Witnesses.
The Moscow branch at the time had been accused of breaking up families, inciting its members to suicide and endangering their lives and health by not allowing its members to have blood transfusions.