Chidambaram also recalled that the affidavit was filed after Ahmedabad Metropolitan Judge S P Tamang's report, which in September 2009, declared the encounter fake.
Later probes, first by SIT and then by CBI, had also said that the deceased had been in the custody of the police and that weapons recovered from them were planted by the policemen.
"The further affidavit has only five or six paragraphs. It does not withdraw the first affidavit. In paragraph two, it says why a further affidavit is being filed and in para 5 it says that the government of India shares intelligence inputs regularly with states. Accordingly, we share intelligence inputs.
The former Home Minister's remarks came amid speculation that the one-member inquiry panel set up by the Union Home Ministry, probing the missing files related to the case of alleged fake encounter of Ishrat Jahan, could submit its report soon.
"It is incomprehensible why some files are missing," the former Home Minister said replying to questions.
Replying to questions, Chidambaram today said,"tell me which part of that affidavit is wrong legally, morally or politically, which sentence or word in the further affidavit was wrong legally, politically and ethically.
"And please remember the further affidavit was vetted by the Attorney General of India.
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