The Jehovah's Witnesses plan to appeal the Russian court's decision in the European Court of Human Rights.
Russia's justice ministry attorney Svetlana Borisova was quoted by the Interfax news agency as saying that the Jehovah's Witnesses "pose a threat to the rights of the citizens, public order and public security".
The court made the ruling after the justice ministry applied for an order to shut down the group's national headquarters near St Petersburg. Some Orthodox scholars view Jehovah's Witnesses as a "totalitarian sect".
"The Supreme Court's ruling to shut down the Jehovah's Witnesses in Russian Federation is a awful blow to freedom of religion and association in Russian Federation", said Rachel Denber, deputy Europe and Central Asia director at Human Rights Watch, in a statement.
The decision to seize the group's assets and close down its St Petersburg head office followed a request from the ministry of justice, which claimed it had found signs of "extremist activity" within the organisation.
"I'm shocked", Yaroslav Sivulsky, who represents the group's administrative centre, told reporters.
"We will do everything possible", he said.
Human rights group Sova has argued that an "official repressive campaign" has been conducted against the movement for years and many of their members have been physically attacked. The religious organization has expanded around the world and has about eight million active followers.
Jehovah's Witnesses have received heavy criticism from mainstream Christianity, members of the medical community, ex-members and others regarding their beliefs and practices.
They take most of the Bible literally and refuse blood transfusions.
In January, the leader of a congregation in the town of Dzerzhinsk in the central Nizhny Novgorod region was fined for distributing materials that authorities deemed extremist, local media reported.
Jehovah's Witnesses will not be able to congregate for worship at their church or anywhere else.
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.