"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.
Mr Pandian had moved the Supreme Court seeking relaxation in his bail condition barring him from leaving Mumbai during pendency of trial, to visit his ailing mother in Gujarat.
The bench took note of Mr Pandian's plea and said it can take up the plea for modification of bail conditions only after the High Court decides his pending applications.
It also asked the trial court to proceed with framing of charges in the case immediately after the pleas of Mr 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.
Mr 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 top court, while granting him bail, had directed Mr Pandian not to leave Mumbai where the trial was going on without permission of the concerned authority.
The IPS officer had moved the Supreme Court in December, 2013 after the Bombay High Court on November 20, 2012 rejected his bail plea.
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