"The court framed charges against 16 accused. Charges were not framed against some of the accused as their applications are pending either in the Bombay High Court or the Supreme Court," said a CBI official.
The matter will be heard by CBI court judge Sunil Kumar Sharma.
The court framed charges against the accused under the charges of murder, abduction, criminal conspiracy, destruction of evidence and relevant sections of the Arms Act.
All the accused pleaded innocence.
The court has till now discharged BJP president Amit Shah, Rajasthan Home Minister Gulabchand Kataria, Rajasthan-based businessman Vimal Patni, former Gujarat Police chief P C Pande, Additional DGP Geeta Johri, Gujarat Police officers Abhay Chudasama and N K Amin.
Besides them, Yashpal Chudasama and Ajay Patel (both senior office-bearers at the Ahmedabad District Co-operative Bank), Gujarat IPS officer Rajkumar Pandiyan and Andhra Pradesh cadre IPS official N Balasubramanyam, Rajasthan IPS official Dinesh M N and Gujarat cop D G Vanzara too have been discharged by the court.
Mr Sheikh was killed in an alleged fake encounter near Gandhinagar in November 2005, after which his wife disappeared and was believed to have been done to death.
Mr Prajapati, an aide of Sheikh and an eyewitness to the encounter, was allegedly killed by police at Chapri village in Gujarat's Banaskantha district in December 2006.
The Sohrabuddin killing case was transferred to Mumbai in September 2012 on the request of CBI for a fair trial.
In 2013, the Supreme Court had clubbed the alleged fake encounter cases of Mr Prajapati with that of Mr Sheikh.