Tax police and other security services spent 16 hours collecting boxes of documents and sealing rooms at the group's headquarters on Thursday and returned Friday to look for more materials and question members.
It was the second raid on the group's Moscow office in less than a year.
Vladimir Bizenkov, an investigator in the prosecutor's office, said the agents came back because they didn't find anything during the raid in April, and would continue searches until incriminating evidence was found.
On Thursday, police refused to let anyone out of the building until late at night, and allowed people to leave only after taking down their names and passport numbers, the group's members said.
"What is going on here is some kind of a nightmare," said Vladimir Turov, a student at the Scientology center.
The tax police said they were investigating possible tax evasion and other financial irregularities, but the Scientologists said authorities had other motives.
"All raids and searches are carried out for a single purpose: to frighten the staffers and force them to renounce their beliefs," said Alexei Danchenkov, a spokesman for the group.
Many Scientologists and human rights activists blame the crackdown on the Russian Orthodox Church, which jealously guards its position in Russia. Authorities have moved against a number of religious organizations following the passage of a 1997 law that placed widespread restrictions on "nontraditional" faiths.
The group's members also said that the participation of Russia's Federal Security Service -- the main successor to the KGB -- in the raids indicated that something beyond an investigation into tax evasion was afoot.
Several agents grabbed reporters, twisting their arms and trying to confiscate film and tape recordings of conversations with the Scientologists.
Bizenkov also demanded that reporters sign a pledge not to divulge "sensitive information related to the investigation." He backed down after a threat to call an attorney.
As in most European countries, Scientology does not have tax-free status as a religious group in Russia, but it is registered as a public movement.
The Scientology center in Moscow is formally called the Humanitarian Hubbard Center, named after the founder of Scientology, L. Ron Hubbard. It holds regular classes, attracting about 200 students each week, according to Danchenkov.
The group charges between $11 and $22 for a month of classes, a basis for the investigation into possible tax evasion.