The issue came to light earlier this week when staff of the special court approached former Special Public Prosecutor Rohini Salian to inquire about whether she had with her some of the confessional statements of witnesses in the case.
"I was surprised when such a query was made to me. The court staff asked whether I had confessional statements of six or seven crucial witnesses recorded before a magistrate.
The witnesses whose statements have gone missing include those of a close aide of Ramji Kalsangra who had "confessed" before a magistrate about the criminal conspiracy hatched to plant explosives in Malegaon in Maharashtra.
Two low-intensity explosions in Malegaon on September 29, 2008, had left seven people dead. The Maharashtra police's Anti Terrorist Squad, which investigated the case before it was handed over to CBI and later to NIA in 2011, arrested a dozen odd accused, including self-styled Sadhvi Pragya Singh Thakur and serving Indian Army officer Lt Col Srikant Purohit.
"You see, this case is being heard in various courts including Supreme Court of the country. There is a possibility that it could have been misplaced and it will be found," he said.
If Worse comes to worst and the statements are not found, the NIA will take the permission of the court and lead the xerox copies of the same statements as "secondary evidence".
Salian, however, contended that statements recorded under 164 are always primary evidence and the files going missing could have a bearing on the case.
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