The registration of all religious groups in Russia had to be renewed after the passage of a religion law in 1997. Any denomination that fails to secure a new registration would be effectively banned from practicing in Russia.
The Justice Ministry took six months to study the literature and operations of the Jehovah's Witnesses, and finally granted registration on Wednesday, church spokesman Alexei Nazarychev said.
"The federal government is trying to follow constitutional principles and support, as far as possible, the freedom of worship," Nazarychev said in a telephone interview. "One can see the difference between (federal policies) and individual bureaucrats who are trying to unleash religious persecution."
The Moscow city prosecutor's office is trying to ban Jehovah's Witnesses from Moscow, using a provision in the religion law that gives courts the right to outlaw religious groups found guilty of inciting hatred or intolerant behavior.
Prosecutors say the Christian group creates rifts between family members because of its practice of not celebrating national holidays, and threatens lives by pressuring sick people into refusing medical aid.
A court hearing against Jehovah's Witnesses was put on indefinite hold in March, when the judge decided to allow experts to study the New York-based group's literature.
The Justice Ministry had its own panel of experts study Jehovah's Witnesses before renewing the church's registration, but the Moscow court refused to use the favorable findings of the federal experts, Nazarychev said.
"It would make a lot more sense to use a panel appointed by the state than to turn to random people," he said. "But the judge said ... we handle our affairs ourselves."
The denomination has appealed, but no ruling has been made yet, he said.
Despite federal registration, individual cities may still outlaw local branches of a religious group.
The Jehovah's Witnesses claim to be the fifth-largest Christian group in Russia, with about 10,000 members in Moscow and more than 250,000 across the country.