Christian anti-persecution charity Open Doors have called the news a “concerning development for freedom of religion and belief” in the country.
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, was banned from distributing literature deemed to break anti-extremism laws last year.
Open Doors have 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 confining religious activity to registered buildings.
Meanwhile, the country has cracked down on a blogger who has been convicted of inciting religious hatred for playing the popular mobile phone game Pokémon Go in a church.
Ruslan Sokolovsky, 22, who pleaded not guilty to the offence, was given a three-and-a-half-year suspended sentence.
Sokolovsky was arrested in 2016, shortly after uploading the video of himself playing the game on his smartphone.
In the video, which has had over 2 million views on YouTube, he ridiculed legal warnings against playing such games in churches: “Who can ever be offended by you walking around a church with your smartphone?”.
The news comes in the same month that a Russian TV channel pulled an episode of The Simpsons off-air after Russian Orthodox Church leaders deemed it offensive.