CBI sources said the FIR was to be registered yesterday but could not be done because of some technical issues and is likely to be registered tomorrow.
They said the agency move is the result of a Punjab and Haryana High Court order directing it to take action against the Dera chief, who is soon going to make his movie debut with "Messenger of God".
A former Dera follower, Hansraj Chauhan, had approached the High Court alleging that he, along with around 400 saints of the Dera, was castrated inside the ashram on the orders of Gurmeet Ram Rahim Singh.
Chauhan had said in the petition that they were assured that those who would get castrated will be able to meet the God through the Dera head.
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Justice K Kannan of the High Court passed the order on the petition ordering a CBI inquiry into the incident.
Taking cognizance of the petition, the HC had earlier ordered medical examination of petitioner Chauhan from the government multi-speciality hospital which found that he has been castrated.
The Dera chief, who is going to hit the big screen next month with his film 'Messenger of God (MSG)', has already courted controversy with Sikh organisations, including Akal Takht, seeking a ban on it.
Gurmeet Ram Rahim is also facing trial in connection with cases of murder of a journalist and sexual exploitation of his women disciples.