"Issue notice to respondents returnable within four weeks," a bench of justices Ranjana Prakash Desai and Madan B Lokur said.
Shah was arrested by the CBI on July 25, 2010 in connection with the case and had spent over three months in Sabarmati Jail in Ahmedabad before being granted the bail.
Besides Shah, suspended Deputy Inspector General D G Banjara, R K Pandiyan (both Gujarat cadre Indian Police Service officers) and Dinesh M N (Rajasthan cadre IPS officer) are main accused in the case.
N K Ameen, then DSP with the Gujarat police, is also an accused in the case. All of them, except Shah, are in jail.
The court's notice came on an application by the CBI which is seeking a direction to get certain documents related to the case. The apex court, on September 27, 2012, had ordered the transfer of the Sheikh encounter case to Maharashtra after the CBI alleged that witnesses were being intimidated and contended that trial cannot be held in a free and fair manner in Gujarat.
Sheikh and his wife Kauser Bi were allegedly abducted by Gujarat's Anti-Terrorism Squad from Hyderabad and killed in a fake encounter near Gandhinagar in November 2005.
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