Baig, who is on the death row, was earlier lodged at the Arthur Road Central Prison in Mumbai. He was shifted to Yerwada Jail in Pune last year as the High Court was not hearing his appeal against conviction.
Baig earlier this year filed an application through his lawyer Mehmood Pracha seeking a direction to transfer him back to the Arthur Road prison as he feared threat to his life in Yerwada Jail.
Baig, in his application, claimed that the environment in Yerwada prison is hostile and he fears that he too shall face the same fate as co-accused in the German Bakery blast case Qateel Siddique, who was attacked and killed inside the jail in August 2012 by fellow inmates.
On February 13, 2010, a bomb exploded inside the German Bakery in Pune's upmarket Koregaon Park area killing 17 people, including five foreigners, and injured 58 persons.
Baig had approached the High Court challenging his conviction and claimed innocence. The appeal is still pending.
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