'It is submitted that evidence collected by NIA in further investigation is not in consonance with evidence collected by ATS and CBI. The court may kindly pass appropriate orders in the matter,' the National Investigation Agency said in its reply before the special court.
The agency said no evidence was found in support of the conclusion drawn in final report filed by ATS and CBI recommending prosecutions of the nine Muslims, arrested in connection with the September 8, 2006 explosions that killed 37 people.
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NIA filed its reply after the arrested persons filed applications seeking discharge from the case.
The special NIA court has now adjourned the case till next month.
Maharashtra ATS had arrested Noorul Huda Samsudoha (28), Shabbir Ahmed Masiullah (41), Raees Ahmed Rajab Ali Mansuri (35), Dr Salman Farsi Abdul Latif Aimi (40), Dr Farogh Iqbal Ahmed Magdumi (38), Mohammad Ali Alam Sheikh (42), Asif Khan Bashir Khan alias Junaid (35), Mohammad Zahid Abdul Majid Ansari (31) and Abrar Ahmed Gulam Ahmed (38). They all were granted bail after NIA took over the probe.
NIA found that blasts were the handiwork of Hindu right-wing group and arrested Lokesh Sharma, Dhan Singh, Manohar Singh and Rajendra Choudhary.
The role of saffron group came to the fore after Swami Aseemanand, an accused in the 2007 Mecca Masjid blast, made a confession in this regard.
The NIA, on May 22 filed a supplementary chargesheet against four Hindu activists and also listed a number findings which contradicted those of ATS and CBI.
Malegaon had seen another terror act in 2008 allegedly by right-wing Hindu groups and Sadhvi Pragya Singh and former Lt Col Srikant Purohit were arrested in that connection.