Russian Orthodox Patriarch Alexis II this week welcomed recent police raids on four premises owned by the Scientologists in Moscow. He said they might "shed light on what these sects inspire in people; charity and peace or confusion and evil".
The Moscow public prosecutor has initiated proceedings against the Scientologists, citing legislation covering commercial activities and religious and social organisations.
Persons found guilty of breaking these laws face from two to three imprisonment and fines.
Media reports say Russian Scientologists might even face the far more serious charge of spying for a foreign country. However the press bureau of the FSB - the successor to the Soviet KGB - , questioned by AFP, declined to comment on the last charge.
"This is just a rumour to discredit us," said Alexei Danchenkov, spokesman for the "Ron Hubbard humanitarian centre" in Moscow. He remarked that "Scientologists have even taken part in activities against the CIA in the United States."
"We pay our taxes and our staff have committed no crime," Danchenkov said.
The FSB which searched the Scientologists' offices in collaboration with tax officials last week, found some 15,000 files of members, some of which were confiscated.
"The majority of these dossiers contain only the address, telephone and details of the courses which our members have attended", said Danchenkov. "Some files contain confidential information" provided by members about their lives, he said.
A former Church of Scientology member who spoke to AFP on condition he not be identified, said that on the orders of the movement's leaders, he had for several months collected "information on those who criticise Scientology, journalists and priests particularly".
He said "the Church of Scientology is not a religious movement and is organised on a military model". Activities of members are limited strictly to learning as much as possible about the doctrine propagated by Ron Hubbard, the movement's founder.
"Denunciations of members by other members are routine practice," he said.
The Church of Scientology is also under close scrutiny in Germany where the authorities say it uses "quasi totalitarian methods". It has also run foul of magistrates in France.
An investigation into the Scientology movement was opened in Russia last April.
"This corresponds to a desire to establish a single ideology in this country, that of the Orthodox religion," said Danchenkov, saying the works of Ron Hubbard were banned by the KGB during the Soviet era. "Certain Orthodox leaders have very close ties with the present regime," he said.
"The Orthodox Church has nothing to do with these police raids," said Alexander Dvorkin, the director of a centre for information about sects, which is close to the Orthodox Church.
"Every day, I get phone calls from people accusing the Scientologists of destroying their families," he said.
The Church of Scientology officially set up shop in Russia in 1993 and claims 30,000 followers in the country.
Last Thursday, Moscow police the head offices of Russia's Scientologist movement as part of an investigation into the group's financial activities in Russia.
Footage shown by Russian television showed armed police storming into the Scientologists' building and checking documents of its US directors.
The police also dispersed a school class attended by several dozen children.
The US head of the Scientologist movement, Reverend Heber Jentzsch protested to the Russian ambassador in Washington saying the raids were "unconstitutional harassment of members of a peaceful religion".
Los Angeles-based Jentzsch said that aside from a "fabricated claim from a 'former member'," the reason for the raid and investigation "remains a mystery".
He hinted hower that Germany may have influenced Russia to take such measures against the church.
"There is strong cause for suspicion that today's raids came about due to German influence," Jentzsch told the Russian ambassador in a letter.
Scientology, founded by the science-fiction writer Ron Hubbard and based in Los Angeles, is recognized as a religion in the United States.
The Russian government last February gave all foreign religious organizations six months to register in accordance with a 1997 law that banned sects with less than 15 years' existence in Russia from actively seeking converts.
Scientology is considered a sect in some western countries, including Germany and Greece, where authorities contend that its leaders seek economic gain.