At present, 22 accused, mostly police personnel from Gujarat and Rajasthan, are facing trial in the case.
Judge S J Sharma said Friday that he will pronounce the verdict on December 21.
"I need about 14 days. I am sure I will finish it by December 21. If I don't complete by December 21, then I will pass the judgement on December 24. But I am very sure that I will be able to complete my work by December 21," the judge said.
Of the 38 people charged by the CBI for the alleged fake encounters, 16, including BJP chief Amit Shah (who was minister of state for home in Gujarat then) and all senior police officials, have been discharged in the case.
Earlier, while recording their statement under Section 313 of the CrPC, most of the accused had claimed innocence and had said they had been falsely implicated by the investigating agency.
Under Section 313, after examination of witnesses, a final chance is given to an accused to record his statement.
"The chargesheet against me was prepared (by the CBI) based on false witnesses. I'm innocent. I have not participated in any police encounter," Abdul Rehman, an accused, had earlier told court.
According to the CBI, Abdul Rehman, then inspector with the Rajasthan Police, was part of the encounter team and had fired at Shaikh.
Rehman had also denied the CBI's claim that he had filed the FIR in Sohrabuddin Shaikh case.
Ashish Pandya, who is accused of pulling the trigger on Prajapati, had told court that he fired in self-defence and was discharging his duty.
"The encounter was genuine. I fired at Prajapati in self defence," Pandya said, adding that he was discharging his official duty.
Pandya, who was then sub-inspector with the Gujarat Police, was part of the Special Task Force to eliminate Prajapati at Chapri village of Ambaji town in Banaskantha district.
Shaikh, a suspected gangster, and his wife Kausar Bi were killed in an alleged fake encounter in 2005 by the Gujarat Police.
His aide Prajapati was killed in another alleged fake encounter in 2006 by Gujarat and the Rajasthan Police.
The case was initially probed by the CID, Gujarat, before being transferred to the CBI in 2010.
During the course of trial, the prosecution examined 210 witnesses, of which 92 turned hostile.
At the conclusion of final argument, CBI counsel B P Raju had pointed out that there were "lacunae" in the central agency's investigation as they got the case five years after the alleged incidents.
The CBI entered into the frame after five years and examination of witnesses began 12 years after the crime was committed due to which there were some "lacuna" in the probe, he had told court.
He added that some star witnesses turned hostile during the trial, hampering the CBI's case.
Responding to the same, the judge had said, "I don't blame CID. I don't blame CBI. There are statements and witnesses. If they come here and say something else, it's not your fault. You did your job."
The case was transferred to Mumbai in September 2012 on the request of the CBI to ensure a fair trial.
The encounter cases of Shaikh, Kausar Bi and Prajapati were clubbed together in 2013 after the Supreme Court directed that the trial be shifted to Mumbai from Gujarat.
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