Gurmeet Ram Rahim Singh, who is serving a 20-year jail term after being convicted in two rape cases, has been charged along with doctors Pankaj Garg and MP Singh.
They allegedly castrated the men at the Sirsa-based Dera, officials said.
The charge sheet has been filed in a special court in Panchkula.
The case relating to the alleged castration of 400 devotees was registered on the orders of the Punjab and Haryana High Court.
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