A bench of Justices A M Sapre and R Banumathi directed the states should file their replies within eight weeks.
Advocate Shobha appearing for NHRC said some states have filed their replies but many of them were yet to do so.
She urged the bench to give these states the last opportunity to file their replies saying that the notices to state governments on the petition were issued in 2014.
It has also sought direction that the state governments should not refuse to comply with the recommendations made by Commission.
The Commission said that due to apex court verdict of 2014 by which certain guidelines were framed, its role in such enquiries has virtually been nullified.
"The said guidelines which are made in sub-silentio, having not considered various mandatory provisions of the Protection of Human Rights Act, 1993, circumscribe and completely abrogate the power conferred on NHRC by the Act, to enquire suo motu or on a petition presented to it by a victim or any person on his behalf into any complaint of violation of human rights by a public servant," the plea said.
It said the Commission has issued guidelines from time to time regarding the procedure to be adopted in cases of encounter killings.
"The latest guidelines were issued by the Commission in May 2010 which provided that an information of encounter killing should be given to NHRC within 48 hours after the incident and a second report along with the post-mortem report, Magisterial Enquiry Report and forensic report should be submitted to the Commission within three months," it said.
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