Some Russian regions have already shut down branches of Jehovah's Witnesses.
The U.S. -founded Jehovah's Witnesses says it numbers about 8 million people worldwide.
Russia's Justice Ministry has filed a case with the Supreme Court to declare the administrative center for Russia's Jehovah's Witnesses an extremist organization.
Jehovah's Witnesses, which according to their global website was first legally registered in 1991 as a religious group in Russian Federation and re-registered in 1999, has faced several legal troubles in the past.
The Russian Legal Information Agency (RAPSI) has also confirmed the legal action.
In response to the latest pressure, Vasily Kalin, chairman of the religious group's steering committee, said members simply want to "peacefully worship their God", according to the press office.
Russian investigators conducted a large-scale inspection of its national headquarters near St. Petersburg earlier this year, carting off many documents. Even after being recognized by the new Russian government, the group continued to face opposition from influential forces in Russian society and the government, which likened the group to a cult that promoted religious hatred, the Los Angeles Times reported in 2001. In 2004, a Moscow court dissolved and banned a Jehovah's Witnesses group accusing the body of recruiting children, inciting suicide and preventing followers from accepting medical assistance, and encouraging followers to break from their families.
Thousands of Jehovah's Witnesses were deported to Siberia during Joseph Stalin's 30-year reign of terror.
In 2009, the Supreme Court of Russia upheld a lower court ruling that declared 34 pieces of Jehovah's Witness literature as "extremist", including their magazine The Watchtower in Russian.
"Extremism is deeply alien to the Bible-based beliefs and morality of Jehovah's Witnesses", the statement said.