Monsignor Jerzy Mazur was the bishop in Irkutsk, in Siberia, but was not allowed back in Russia a year ago after a trip abroad.
Mazur, a native of Poland, was one of five Roman Catholic clerics barred from the country last year amid tension over the church's activities in predominantly Orthodox Russia. The Russian Orthodox Church complains that Roman Catholics are poaching converts from people who traditionally would have been Orthodox adherents.
The strains have blocked efforts by Pope John Paul II to make the first papal visit ever to Russia.
Mazur also raised the ire of the Foreign Ministry by using the Japanese name of Karafuto Prefecture to identify the region in his diocese encompassing the southern part of Sakhalin Island and the disputed Southern Kuril Islands. Russia seized the islands from Japan at the end of World War II.
The Vatican said Mazur was transferred to Elk, Poland, and will be succeeded in the Russian diocese by Bishop Cyryl Klimowicz, a native of the former Soviet republic of Kazakhstan.
The moves comes amid reports the Vatican is seeking to arrange a papal stopover in Russia when John Paul visits Mongolia in August.