Russian Supreme Court spokesman Pavel Odintsov said it rejected the group's appeal of September's ruling by a regional court in Rostov-on-Don. That ruling outlawed the group's activities in the region, seized its assets there and labeled 34 of its publications as extremist.
The group said the list of books includes a children's book of Bible stories, and its signature magazine, The Watchtower.
"We are deeply disappointed with that decision," Jehovah's Witnesses spokesman Yaroslav Sivulskiy told The Associated Press. "We are concerned that it may affect all our activities, including imports of our publications which are printed in Germany."
Sivulskiy said that the Supreme Court specifically ruled that the 34 publications should be added to the federal list of publications considered extremist. He said that would effectively ban the publications throughout Russia.
"We consider it to be a rollback to the past," Sivulskiy said in a reference to the Soviet past when many members of Jehovah's Witnesses, including his father, were put in prisons. "The Supreme Court makes it illegal for us to profess our views."
He said that the group will appeal the Supreme Court's verdict to the European Court for Human Rights, arguing that the Russian courts misinterpreted the law. The law on combating extremism that served as a basis for the verdict has been widely criticized by many rights groups, which said its loose phrasing allowed authorities to stifle dissent.
A 2004 ruling by the Moscow City Court prohibited Jehovah's Witnesses branch in the Russian capital from engaging in religious activity in the Russian capital.
Sivulskiy said there are at least 160,000 Jehovah's Witnesses in Russia.