"The discharge application of Agarwal is rejected," said a senior CBI official without elaborating.
Agarwal was the Superintendent of Police, Banaskantha, in December, 2006 when Prajapati was killed allegedly in a staged encounter. He was later arrested by Gujarat CID.
According to CBI, he was the main conspirator in the encounter.
The court has so far discharged BJP president Amit Shah, former Rajasthan Home Minister Gulabchand Kataria, marble trader Vimal Patni, Gujarat Additional Director General of Police Geeta Johri and former Gujarat police chief P C Pande from the case.
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He was killed in an allegedly fake encounter near Gandhinagar in November, 2005 after which his wife went missing and was believed to have been done to death.
Tulsiram, an aide of the gangster and an eyewitness to the encounter, was allegedly killed by police at Chapri village in Banaskantha district in Gujarat in December 2006.
The Sohrabuddin killing case was transferred to Mumbai in September 2012 at CBI's request for fair trial.