The chargesheet names 19 others, including former state DGP PC Pande and current additional DGP Geetha Johri, as accused. Shah and the others have been booked for murder, criminal conspiracy, abduction, illegal confinement, extortion and destruction of evidence.
Additional chief judicial magistrate AY Dave accepted the chargesheet and kept the issue of taking cognisance pending till the court verified the document. The court posted the next hearing to October 10.
Shah was the MoS for home in the Modi cabinet when the police shot Prajapati in December 2006.
According to the CBI, Prajapati was the lone eyewitness to the abduction and staged encounter killings of Sohrabuddin Sheikh and his wife Kauser Bi in November 2005.
Shah is also the prime accused in the murders of Sohrabuddin and his wife.