As the influence of religion on society diminished in the Western world, the need for the civil authority to share its power with the religious authority also diminished. Secularism and state atheism evolved to coexist with religious authority or deny it altogether as in the Soviet Union. However, the Soviet Union eventually modified its approach to the religion and used religious institutions to control and steer the believers. 

President Putin being raised as a KGB officer knows very well how to use religion in imposing the perspective of the state authority. There are also strong suspicions that Patriarch Kirill of Moscow who quickly rose in the Orthodox Clerical hierarchy during the 60s and 70s was also a KGB agent. Patriarch is not only because of his status but also actively participating in public debates has significant influence on the public opinion. After his elevation to the Patriarchy in 2009, through a series of reforms in the church institution made himself the absolute leader of the church. He is the spiritual guide of the Orthodox Christians to support the policies of the State. Indeed he is a fervent supporter of the decisions of President Putin, including full scale invasion of Ukraine and annexation of Crimea.

On the other hand Muslim communities of the Russian Federation have several muftiates and grand Mufties to guide them. Each of the muftiats controls an extensive network of organisations spread out in the Russian Federation including the unlawfully annexed regions. However still some Muftiates remain to be autonomous and many conflicts between the organisations prevent the unification. The fragmented nature of the spiritual administration prevents them from becoming a real strength but also denies the state of this power. 

Moreover the fragmentation in the state-controlled Muftiat seems hard to resolve because of the large amounts of finances these institutions receive through the central authority and donations that create lucrative opportunities for administrators. 

Even without a strong hierarchy there is evidence that state-controlled muslim spiritual organisations are useful for the Russian Federation as much as the Patriarchy. First of all these muftiates give statements in support of the state authority to legitimise even the use of torture by the security forces and also the invasion of Ukraine. Moreover there are cases that their administration collaborated with the Russian security forces collecting information or demanding the closure of the mosques that deviated from the norms established by the administrations.

The deviation from the norms is especially dangerous for the authority because it allows formation of the uncontrolled communities - jamaats. The solution is to condemn them as radical muslims which is especially the case for the Crimean Tatars. After the occupation of Crimea Tatar community that resisted the Russian- controlled muftiate was targeted with the accusations of terrorism. Moreover the intimidation of Tatars in the region also included the distribution of the summons to the army at the exit of the mosques. Russian control of the local muftiate is also used to find collaborators to bring accusations of terrorism. The stigmata of radicalism also brings a certain untouchable status to the victims that diminishes the foreign human rights involvement. 

The latest pogroms in the Northern Caucasia gave the opportunity to present the Muslim community as having a tendency to radicalise and also having strong anti-semitic tendencies. As the state has a strong control on media and muftiats, its involvement in the protests could not be denied. Moreover, as the Chechen leader uses the beating of Koran burning Volgograd resident in Chechnya and his trial to enforce his heroic persona, it also develops the bogeyman characterization of Islam. 

Indeed Islamophobic attacks provoked by the Middle-Eastern style of dressing increased in Russia. The reaction to the special style of attire which was previously denounced by the Mufti of Chechnya, enforces the idea that non-conformism to the state-controlled muftiats is dangerous. 

State control of religion in the Russian Federation is as important as in the Soviet Union. Although the control of Orthodox Church is well established while the control of the Muftiats is more chaotic due to the fragmentation. State controlled muftiates strength is tried to be consolidated  through intimidation and alienation of the Muslim community which was never really accepted by the Russians as the equal citizens of the Federation.