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.
Vanzara said the statements of witnesses recorded by the CBI were "highly suspicious". Prima facie there was no evidence to prove that the encounter was the result of a conspiracy hatched in his chamber, as mentioned in the charge sheet, his plea said.
"... Because the investigation was transferred... with political motives, the CBI has twisted the entire version," he said in the application.
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.
Gujarat Police had claimed the four had links with terrorist organisations, and wanted to kill Modi.
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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