Special CBI Magistrate Raghvendra Singh Chouhan in his order yesterday also dismissed CBI's application to close the case.
CBI had said in its report that it had found evidence against the then Inspector Rajendra Ghule and Sub-Inspector Ramesh More of Mumbai ATS in connection with the disappearance of the witness Dilip Patidar.
The agency sought closure of the case citing absence of requisite sanction from competent authority to prosecute the duo.
However, the magistrate said the alleged act was not a part of their duty as public servant and therefore no sanction is required.
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According to the complainant, ATS took Patidar with them from Indore for questioning on the intervening night of November 10 and 11, 2008 but after that he went missing.
The Madhya Pradesh High Court had transferred the case to CBI on a petition filed by Patidar's brother Ramswaroop.
Ramswaroop's lawyer J P Sharma said that Patidar's family doesn't know whether he is alive or dead and for the last 8 years they have been undergoing tremendous anguish.
At one point of time, he had been a tenant of the absconding accused in the case, Ramchandra Kalsangra.
Earlier this month, National Investigation Agency, probing the blast case, dropped the names of Sadhvi Pragya Singh Thakur and five others as accused in its charge sheet filed before a Mumbai Special Court.
Seven people were killed in twin blasts when people were coming out of prayers during Ramzan on September 29, 2008.