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".
Reacting to the decision, Open Doors UK posted on Twitter: "This is a concerning development for freedom of religion and belief in #Russia."
The Supreme Court ordered that the Jehovah Witnesses' Russian headquarters and 395 local bases be closed, and its property be seized.
According to the Interfax news agency, justice ministry lawyer Svetlana Borisova said in court that the Jehovah's Witnesses "pose a threat to the rights of the citizens, public order and public security".
The group, which claims to have 170,000 followers in Russia, has already come under pressure in the last year; it was banned from distributing literature deemed to break anti-extremism laws.
Last summer, Open Doors UK urged Christians to pray that the Russian government would guarantee constitutional freedoms for a person to share their faith after President Vladimir Putin signed new legislation which confining religious activity to registered buildings.
Thursday's Supreme Court ruling has also been criticised by Human Rights Watch.