A bench headed by Chief Justice TS Thakur passed the order on a Public Interest Litigation for the apex court monitoring of the probe by the SIT.
Senior Supreme Court lawyer Harvinder Singh Phoolka had earlier said that the missing files of the SIT related to the riots had no bearing with the current SIT formed by the Centre.
The files had been ordered by Aam Aadmi Party leader and Delhi chief minister Arvind Kejriwal.
According to reports, a file on constitution of the SIT to probe the 1984 anti-Sikh carnage has reportedly been missing from the Delhi home department since March 16 last year.
The file was reportedly marked to the then city home minister Jitender Singh Tomar, now on bail in a case over his fake degrees.
The 'missing file' issue has surfaced at a critical juncture for the Aam Aadmi Party, as it plans to contest the 2017 Punjab assembly elections.
The AAP government has time and again raised the 1984 anti-Sikh riots issue.
It had recently given an additional Rs. 5 lakhs in compensation to families of the riot victims.
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