"Anti-Church forces fear the rising role of the Church in the country. Such people are few in numbers but some of them wield influence and are ready to use their resources to discredit the clerics," the statement said.
The Church said it was also being ostracized by "those pushing through radical liberal values" for its stern opposition to homosexual marriages, consumerism, the spread of violence and adultery.
The statement could help Putin, who will be inaugurated as president on May 7, to further discredit his opponents among liberal intellectuals eroding their support base among the nascent middle class.
The public debate over the Pussy Riot incident exposed a rift in the Church between the more liberal clerics who called for forgiveness and hardliners who wanted the performers to be severely punished.
The Council sided with the hardliners in the statement saying that the lack of repentance could only "push the sinners into committing their sins again".
Endorsed by Kremlin leaders as Russia's main faith, the Orthodox Church has grown increasingly powerful and rich after the 1991 collapse of the Soviet Union where religion clashed with Communist ideology and was barely tolerated.
Putin and President Dmitry Medvedev as well as their wives Lyudmila and Svetlana openly practice their faith. Putin sought the blessing of a famous Byzantine icon in a remote monastery before embarking on the election campaign.
(Reporting by Gleb Bryanski; Editing by Kevin Liffey)