The nine Muslim accused had sought discharge from the case last year on the ground that the NIA had arrested the right-wing Hindu group members, who purportedly carried out the blasts.
On September 26 last year, the special NIA court had directed the CBI to file their reply in connection with the discharge plea.
"Since the NIA has carried out that investigation and filed a charge-sheet on the basis of the material collected by them during further investigation, it would be appropriate if NIA is directed to file their views in the matter," said the application filed by the CBI.
However, the ATS sought four weeks' time to file their say in the case.
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Special Judge Y D Shinde had directed CBI and ATS to file their replies after one of the accused related to a right-wing Hindu group, also arrested in the case, moved an application to the court praying to summon the ATS and CBI who has previously filed a report accusing members of the banned organisation- SIMI- behind the blast.
It can be recalled that NIA in August last year did not object to the discharge applications filed by nine Muslims arrested.
"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 NIA had said.