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.
Following the ruling, a Jehovah's Witnesses spokesperson announced that they will appeal the decision taking the case to the European Court of Human Rights.
Open Doors UK spoke out after the country's Supreme Court heeded a request by the government to recognise the Jehovah's Witnesses movement as "extremist".
Earlier, the Russian Ministry of Justice applied for an order to shut down the organization's national headquarters near St. Petersburg.
"We fear that people will end up in jail", he said.
Since 2009, 95 materials distributed by the organization in Russian Federation have been declared extremist and 8 Jehovah's Witnesses' branches have been liquidated.
The plaintiff, the Russian Justice Ministry, cited the group's aversion to blood transfusion on religious grounds as reason for the ban. A spokesman, Vasily Kalin, said: 'The Justice Ministry not only humiliates itself and its functions, but has humiliated the entire state in the eyes of the worldwide community with an unreasonable and reckless accusation'. Judge Yury Ivanenko said the court also ruled to seize the center's property.
The Supreme Court's ruling has not taken effect yet.
The court declared Jehovah's Witnesses an extremist organization and banned its 175,000 adherents from congregating on Russian territory.
Tass reports that a court in Moscow on October 12, 2016 warned Jehovah's Witnesses over what it ruled was extremism.
Jehovah's Witnesses do not observe Christmas, Easter, birthdays and other holidays, which they consider to have pagan origins that are not compatible with Christianity.
Still, some Russian evangelicals see the repression of Witnesses as reason to worry, according to William Yoder, spokesman for the Russia Evangelical Alliance.
"We will do everything possible", Sergei Cherepanov, a Jehovah's Witnesses representative, was quoted as saying by the Interfax news agency.
Under Russian law, the ban would not prohibit individual believers from following their creed, but congregating and proselytizing would become offenses punishable with up to five years in prison.
To human rights and religious freedom advocates around the world, the move comes as a major blow.
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