In its reply before the special CBI court here, the central agency said there was evidence against Pandey which established his direct as well as indirect involvement.
The CBI also said it was still collecting evidence and recording statements, as the trial is yet to begin.
The alleged encounter took place when Pandey was holding a high position in the Gujarat Police, CBI pointed out.
Judge J K Pandya then posted the matter for final order on March 16.
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None of the 105 witnesses examined by the court named him, he said.
Pandey, now out on bail, also pointed out that a supplementary charge sheet filed by the CBI, in which Intelligence Bureau officials including the retired special director Rajinder Kumar were named as accused, is yet to be taken on record by the court.
In the first charge sheet filed in 2013, CBI named seven Gujarat Police officers including the IPS officers Pandey, D G Vanzara and G L Singhal.
Police termed them as terrorists, but the HC later ordered a CBI probe which found the encounter to be fake.