The order was passed by a bench headed by Justice V M Kanade who heard a petition filed by Baig who claimed he feared a threat to his life in the Yerwada prison.
The court also ordered the Pune Jail Superintendent to ensure Baig's safety until he is transferred to Nagpur jail.
Baig, who has been sentenced to death, was lodged at the Arthur Road jail in Mumbai but was shifted to Yerwada Jail last year since the High Court was yet to take up the hearing of his appeal against conviction in the 2010 Pune German Bakery blast case.
Baig's counsel, Mehmood Pracha, filed an application seeking transfer of his client back to Arthur Road Jail on the ground that he feared a threat to his life in Yerwada Jail.
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Earlier, the High Court had asked Additional Director General of Police (Prisons) to state whether shifting Baig to some other prison was possible.
"The high security Mumbai Central Prison is already overburdened. There is hardly any scope for segregation of prisoners who cannot be kept together," Desai said.
"Baig has been lodged at the high security cell (in Yerwada Jail) where there is no danger to his life at all," Desai said.
In his plea, Baig had claimed that co-accused Qateel Siddique was murdered inside Yerwada Jail by some inmates in August 2012 and that he too could meet the same fate.