"On one hand you want variation of the bail order for going to Gujarat, but on the other hand, the trial is stayed by the Bombay High Court on your applications," a bench of Justices Ranjan Gogoi and N V Ramana said.
Pandian had moved the apex court seeking relaxation in his bail condition barring him from leaving Mumbai during pendency of trial, to visit his ailing mother in Gujarat.
It also asked the trial court to proceed with framing of charges in the case immediately after the pleas of Pandian were decided by the High Court. The High Court has also stayed the trial proceedings.
The court had last month allowed the accused officer to visit his ailing mother in Ahmedabad for seven days.
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Pandian, who was granted bail on March 28 last year, is facing charges in the case in which Sheikh and his wife were allegedly abducted by Gujarat's Anti-Terrorist Squad from Hyderabad and killed in an alleged fake encounter near Gandhinagar in November 2005.
The IPS officer had moved the apex court in December, 2013 after the Bombay High Court on November 20, 2012 rejected his bail plea.
Pandian, along with IPS officer Abhay Chudasma, Rajasthan cadre IPS officer M N Dinesh and some other policemen, were lodged in Taloja jail in Navi Mumbai after the Supreme Court transferred the trial in the case to Mumbai from Ahmedabad.