A bench headed by Justice Ranjan Gogoi issued notice and asked the Centre, the Madhya Pradesh government and the CBI to reply to the plea which has also sought a court-monitored probe by an independent agency like a special investigation team (SIT or the CBI.
The plea was filed by Mehmooda Mohammed Salim Mucchhale, a relative of one of those killed.
It also said they were not permitted to cross-examine the version of the police officials.
The petition raised the question whether the one-man commission formed was only to "hush up the case".
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The high court had on February 21 dismissed the plea of the petitioners holding that several directions had been passed in other similar petitions.
The plea also questioned the promotion and instant rewards given by the state government to the police officials involved in the encounter, saying it was against the spirit and directions of the apex court.
The eight SIMI activists, who escaped from the Central Jail in Bhopal, were killed on October 31, 2015 in an alleged police encounter.
The activists had escaped from the jail after killing a security guard and scaling the prison wall with the help of bedsheets, following which some officials responsible for jail security were suspended.
They were identified as Amzad, Zakir Hussain Sadiq, Mohammad Salik, Mujeeb Shaikh, Mehbood Guddu, Mohammad Kalid Ahmed, Aqeel and Majid.