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 M P Singh.
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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 agency had registered the case of alleged criminal conspiracy for voluntarily causing grievous hurt by dangerous weapons or means among other charges under the Indian Penal Code against Gurmeet Ram Rahim Singh and others in 2015.