In his application, Dayanand Pandey said his name was Sudhakar Dwivedi and his arrest was the result of mistaken identity.
The special court for National Investigation Agency (NIA) rejected the application filed by Pandey, said special prosecutor Avinash Rasal.
After he took 'sannyas' (renounced the world), he came to be known as 'Swamy Amrutanand' and later as 'Shankaracharya', he said.
However, Rasal argued in the court that during his arrest, while signing arrest form, he never disputed that he was Dayanand Pandey, nor did he say anything when produced before a magistrate.
Six people were killed and nearly 100 others injured when a bomb strapped to a motorcycle went off at Malegaon in Nashik district of Maharashtra on September 29, 2008.
Twelve people, including sadhvi Pragya Singh Thakur and Army officer Prasad Purohit, were arrested in connection with the blast in the town which has sizable Muslim population.
The NIA earlier this year gave a clean chit to Thakur, following which she obtained bail.
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