The disgraced cult leader, who is lodged in Rohtak's Sunaria jail on charges of rape, appeared via video- conferencing. He has been named as the main conspirator in the cases.
His driver, Khatta Singh, approached the court seeking to record a fresh statement against the sect head, his counsel Navkiran Singh said.
Khatta, a witness in the murder cases, had retracted his statement in 2012. He had turned hostile as he was under pressure from Ram Rahim and his "goons", Navkiran alleged.
The CBI court is hearing the cases of killings of journalist Ram Chander Chhatrapati and former Dera manager Ranjit Singh.
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Chhatrapati was shot at in October 2002 after a newspaper owned by him, 'Poora Sach', published an anonymous letter narrating how women were being sexually exploited by the sect head at the Dera headquarters.
Ranjit was allegedly shot dead in July 2002.
According to the prosecution, he was murdered for his suspected role in circulating the anonymous letter which made the allegations of sexual exploitation.
The CBI judge granted permission for video-conferencing yesterday after Panchkula DCP Manbir Singh moved an application, contending that they cannot bring the Dera chief in person due to law and order problem.
Contingents of paramilitary troops and the Haryana Police have been deployed in Panchkula as security arrangements were tightened ahead of the hearing.
On August 25, after the CBI court convicted Ram Rahim for raping two of his female disciples, violence erupted in Panchkula and Sirsa in which 41 people died. The court sentenced him to 20 years in prison on August 28.