Police discovered 27 children and 38 adults living in catacomb-like cells in an eight-level underground bunker.
The sect's elderly leader, Faizrakhman Sattarov, had reportedly wanted to build his own Islamic caliphate beneath the ground.
Prosecutors said some of the children had lived there for more than a decade.
The sect was uncovered last week in a suburb of the city of Kazan during an investigation into recent attacks on Muslim clerics in Tatarstan, a mainly Muslim region on the River Volga.
Mr Sattarov, who had declared himself a Muslim prophet, has been charged with the crime of "arbitrariness", a broad crime that covers "actions contrary to the order presented by a law".
No immediate reaction to the charges was reported.
Officials said the children, aged between one and 17 years, had never left the compound,
According to the Russian website Islam News, Mr Sattarov, 83, declared himself an Islamic prophet in the mid-1960s after interpreting sparks from a trolleybus cable as a divine light from God.
He and his followers began to shun the outside world in the early part of this century.
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