The ruling party also took a swipe at Congress over its demand for a Supreme Court-monitored probe and said during the UPA rule, "no evidence" could be collected in the case that dragged on for years.
The charges were dropped in accordance with the laws, party national secretary Shrikant Sharma said about the NIA giving a clean chit to Pragya and removing charges under MCOCA against another key accused Colonel P S Purohit.
"Congress leaders had insulted the Supreme Court by questioning the hanging of (1993 Mumbai blast convict) Yakub Memon and (2001 Parliament attack convict) Afzal Guru. Now they are seeking a SC-monitored probe even though everything has happened in the Malegaon blasts as per law," Sharma said.
He claimed that stringent MCOCA charge was dropped against some accused on the court's directions.
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BJP spokesman Nalin Kohli, while rejecting the Congress allegation of "direct interference" by PMO in Malegaon case, charged that during UPA's 10-year rule, the investigative agencies were not allowed to do their job.
"Under Prime Minister Modi's government, no interference is there. The courts are reposing faith in the agencies, no castigation is there," he said.
Kohli said if the agency finds there is lack of evidence on the basis of which to proceed "which may have been driven by political reasons under the Congress, they will now obviously make those corrections."