The accused persons had approached the apex court challenging the denial of their bail,.
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Six people were killed and over 100 injured when an explosive device strapped on a motorcycle went off near a mosque in Malegaon, a town about 200 km from Mumbai in north Maharashtra, on September 29, 2008.
A bench comprising Justices J Chelameswar and A M Sapre asked the Centre and NIA to file their responses within one week.
It discharged three accused -- Shyam Sahu, Shivnarayan Kalsangra and Praveen Takalki -- from the case.
A Supreme Court judge on Friday recused from hearing a plea against removal of Special Public Prosecutor by NIA in the 2008 Malegaon blasts case, saying that he had represented certain accused in the matter.
Six people were killed and over 100 injured when an explosive device strapped on a motorcycle went off near a mosque in Malegaon, a town about 200 km from Mumbai in north Maharashtra, on September 29, 2008.
Special NIA Judge V S Padalkar last month directed all the accused, including Thakur, to appear before the court at least once a week.
He said he's languishing in jail for nine years without even charges being framed against him.
However, the certified copy of the said order was issued by the court only on May 1, 2015.
The National Investigation Agency has accused the Maharashtra Anti-Terrorism Squad of planting evidence and coercing witnesses, but its own investigation is incomplete and leaves many questions unanswered.