Now, the government of President Islam Karimov is taking a broader aim against believers -- this time targeting primarily fringe Christian missionary groups.
A recent documentary on Uzbek state television condemned such groups as the Jehovah's Witnesses, Christian Gospel Church, and Blagodat (Grace) as creating a "global problem, along with religious dogmatism, fundamentalism, terrorism, and drug addiction."
The documentary, "In the Clutches of Ignorance," featured several Uzbek religious and political experts, state officials as well as representatives of the Orthodox and Catholic churches in Uzbekistan. All took a critical view of missionaries.
Jasur Najmiddinov, a theologian from Uzbekistan's Islamic University, was among the many religious experts interviewed. Najmiddinov accused Christian missionary activities, especially by Protestant groups, of becoming a "political tool" and a "part of geopolitical games."
"Their center or place of origin traces back to the United States," Najmiddinov says. "They have even gone so far as meddling in politics. We all know representatives of the Protestant movement played a significant role in the Orange Revolution in Ukraine."
In an interview with RFE/RL's Uzbek Service, Najmiddinov later said that Christian missionary movements are a "hidden threat to Uzbek society" and that their activities are "as dangerous as terrorist activities or the illegal drug trade."
The Uzbek theologian added: "Missionaries' activities here can lead to disruptions in our society. If a member of an Uzbek family -- our family member or one of our relatives -- change their faith, the family would not tolerate it."
The documentary also showed video footage of people gathering and praying. It said Uzbek Christian converts, having betrayed their Islamic faith, could easily betray their country, too.
Uzbek law prohibits all religious missionary activity, unregistered religious groups, and the unapproved publication of religious literature.
Defenders of religious freedom, such as the Norway-based group Forum 18, say there has been a steady rise in repression against religious communities in Uzbekistan, including police raids on private homes, detentions of believers and converts, and deportations of foreigners involved in religious activities.
According to Forum 18, a young female Jehovah's Witness was detained and physically assaulted by a police officer after a raid on a private home in the city of Samarkand in March. In another police raid in Samarkand on April 3, security forces detained a Christian convert, Bobur Aslamov. He remains missing. Forum 18 also says several other Protestant church members were beaten during the raid and that police seized Christian literature as well as a laptop computer.
On April 9, police in Tashkent reportedly raided a service held by a group called the Full Gospel, an offshoot of Pentecostalism. Church leader Serik Kadirov was arrested along with four others. They were released the following day.
The state television documentary, broadcast on May 16, accused missionaries of targeting "those with low political awareness and weak-willed young people, as well as minors." It added that missionaries that "get funds abroad" undermine the Uzbek people's Islamic faith and values.
Islam, But Only Government Islam
That's a charge that strikes many as ironic, however.
Religious-freedom defenders and Uzbek government critics say the country's Muslim community is more tightly controlled than any other religious group in the country. Activists say hundreds of ordinary Uzbek Muslims are put behind bars on a regular basis for merely practicing their religion.
Obidkhon Qori Nazarov, a prominent Uzbek imam, tells RFE/RL's Uzbek Service that he blames the Uzbek government's pressure on Muslims for alienating many Uzbeks from their centuries-old faith.
"This is the result of the government's policies. The government is not leaving Muslims alone," Nazarov says. " People are being fired from their jobs or expelled from universities for merely growing a beard or wearing head scarves. Some people are even sent to prison. People are afraid of following the most basic Islamic requirements. For instance, parents do not allow their children to pray or to go to mosques, because they are afraid of the government."
The Uzbek government maintains that Muslims, Christians, and followers of all other religions enjoy full freedom in following their faith. However, government critics such as Nazarov say the government controls all religious activities -- and that even imams are appointed by authorities.
"It's like Soviet times," Nazarov says. "In the Soviet days, we also had mosques and churches everywhere. But in reality, they all operated under the tightest government control."
RFE/RL's Uzbek Service contributed to this report