The CBI court in Panchkula on August 28 had sentenced Ram Rahim to 20 years in prison after his conviction.
"We have filed an appeal today in the Punjab and Haryana High Court. Through this, we have challenged the order of the CBI court," defence counsel Vishal Garg Narwana said here.
He said the CBI verdict has been challenged on several grounds.
"One of the grounds was that there was a delay of more than six years in recording the statements of the women (victims) by the CBI after the incident," the defence counsel said.
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He alleged that the CBI had also concealed some portion of the victims' statement.
Ram Rahim was convicted by the special CBI court on August 25, following which violence and arson had erupted in Panchkula and Sirsa districts which left 41 people dead and scores of injured.
The judge pronounced two sentences of 10 years rigorous imprisonment in each of the two rapes that date back to 2002.
The controversial sect head is currently lodged in Sunaria jail in Rohtak district of Panchkula.
In May 2002, the high court directed the Sirsa district and session judge to probe the allegations in the letter. In September 2002, the high court handed over the matter to the CBI after the district court indicated the possibility of sexual exploitation
In December 2002, the CBI registered a case of rape, criminal intimidation against Ram Rahim.
The CBI filed a charge sheet against the Dera head in Ambala court in July 2007. The charge sheet mentioned the sexual exploitation of two 'sadhvis' between 1999 and 2001.