Special CBI judge J K Pandya issued notice to the CBI yesterday, seeking reply by March 28.
Vanzara, one of the prime accused, said in his plea that the charge sheet filed by the agency was "concocted" and there was "no prosecutable material" against him.
The former deputy inspector general of police also sought discharge on the ground of 'parity', as former in-charge director general of Gujarat Police P P Pandey has been discharged from the case.
"... Because the investigation was transferred... with political motives, the CBI has twisted the entire version," he said in the application.
Even the then chief minister Narendra Modi was questioned by the investigation officer in a bid to make him an accused, it said.
Ishrat, a 19-year-old girl from Mumbai, Javed Shaikh alias Pranesh Pillai, Amjadali Akbarali Rana and Zeeshan Johar were killed in an alleged encounter with police on the outskirts of Ahmedabad on June 15, 2004.
But a special investigating team set up by the Gujarat High Court concluded that it was a fake encounter. Following which the high court transferred the case to the CBI.
In the first charge sheet filed in 2013, the CBI named seven Gujarat Police officers including IPS officers P P Pandey, D G Vanzara and G L Singhal for kidnapping, murder and conspiracy.
Vanzara was last year discharged in the Sohrabuddin Sheikh and Tulsiram Prajapati fake encounter cases.
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