Sadhvi Pragya and Lt Col Purohit were charged with plotting the 2008 Malegaon blasts.
A local court has issued an arrest warrant against two officers of Maharashtra ATS in connection with the disappearance of a witness in the 2008 Malegaon blast case.
Special CBI Magistrate Raghvendra Singh Chouhan in his order on Thursday 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.
The court also said that prima facie there is evidence against Inspector Ghule and More for their prosecution for criminal conspiracy, kidnapping, fabrication of evidence and other offences under IPC.
According to the complainant, ATS took Mr 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 Mr Patidar's brother Ramswaroop.
Ramswaroop's lawyer J P Sharma said that Mr Patidar's family doesn't know whether he is alive or dead and for the last 8 years they have been undergoing tremendous anguish.
According to ATS, Mr Patidar was released on November 18, 2008 and was asked to come back with certain documents but he never returned.
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.