A bench comprising Chief Justice Dipak Misra and Justice A M Khanwilkar asked the lawyer appearing for the agency to take instructions on conducting the probe and providing of adequate compensation sought by the petitioner.
Gulbahar Bibi, wife of 50-year-old Afrazul Khan, has also sought a direction that the video of her husband's ghastly murder and setting him ablaze be withdrawn from the internet and social media sites.
The top court, however, said it would look into the issue at a later stage.
Earlier, the apex court had termed as "horrendous" the video of the labourer being hacked and burnt alive in Rajasthan's Rajsamand district on December 6 last year.
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Sheikh's widow is seeking an impartial probe by a central agency into the murder, besides withdrawal of the video from being circulated on the internet.
Jaising had said the video has already been seen by millions of people and a direction be issued to the Centre and the state government to ensure that it was not circulated any further and withdrawn from the internet.
The plea sought appointment of special public prosecutor to conduct the trial and transfer of the investigation to Malda district in West Bengal where the petitioner resides.
Khan, who hailed from West Bengal, was allegedly hacked and burnt alive on December 6 last year and the entire murder was recorded on camera by the minor nephew of accused Shambhulal Regar, who is in judicial custody.
Regar, after killing Sheikh, was allegedly seen on the video ranting that he did it to 'stop Love Jihad', a term publicised to refer to Muslim men marrying Hindu women.