Gujarat government had appointed former apex court Judge MS Shah in April last year to monitor the investigation into the killings in the alleged fake encounters within the period.
"Having regard to the fact that a monitoring authority has been put in place and a former judge of this court is its chairman, we desire the chairman to look into all instances of the alleged fake encounters mentioned in the two writ petitions.
"We want the investigation to be thorough so that truth in each case is revealed," a bench comprising Justice Aftab Alam and Justice CK Prasad said while hearing the petitions relating to alleged fake encounters in Gujarat between 2002 to 2006 which purportedly showed a pattern that people from the minority community were targeted as terrorists.
The bench said it will be open for the chairman of the monitoring authority to constitute an independent team either with officer from Gujarat Special Task Force (STF) or from outside.
The court said it will also be open for the chairman of the monitoring authority to call for earlier police and case records or records from human rights bodies in respect of any encounter death, which has been mentioned in the writ petitions.
However, the bench clarified that monitoring authority will not go into the cases which are being investigated by other agencies on orders of the apex court.
It also said that the chairman of the monitoring authority, if so desires, could give hearing to petitioners in the case or kin of the victims of encounter deaths.
The judges said the petitions on the issue were pending for several years but no substantive order was passed till date and subsequent developments like appointment of STF and setting up of monitoring authority had taken place during the pendency of the matter. The apex court was hearing two PILs filed by veteran journalist BG Verghese and poet and lyricist Javed Akhtar.
Verghese had sought an inquiry into 21 alleged fake encounter killings by the police in Gujarat during the period.
Akhtar had sought a probe by a special investigation team (SIT) into the alleged fake encounters in the state, claiming that innocent people, particularly from Muslim community, were being targeted as terrorists.
Verghese had said the pattern of killings showed there was a need for investigation and sought a direction to the Centre and Gujarat government to order an inquiry into the encounter killings and compensation to the next of the kin.
Akhtar, in his petition, had cited news reports and a sting operation done by a news magazine into the killing of an alleged criminal Sameer Khan in October 2002.
He had alleged it was a fake encounter and there was an attempt for its "cover up" by the Gujarat government.
Khan, who was in police custody, was killed on the intervening night of October 21-22, 2002, when he allegedly snatched the revolver of a policeman who had accompanied him with a team to a spot where he had allegedly murdered a constable.
An FIR was registered alleging that Khan was involved in a conspiracy hatched by Pakistan's Inter Services Intelligence (ISI) and Jaish-e-Mohammed (JeM) to assassinate Gujarat Chief Minister Narender Modi and other leaders.
Akhtar, who jointly filed the petition along with social activist Shabnam Hashmi, had alleged it was the same team of Gujarat police which allgedly killed Sohrabuddin Sheikh in the fake encounter and later murdered his wife Kauser Bi.
Their petition, filed through advocate Prashant Bhushan, had contended there were other media reports of killings of innocent persons in fake encounters by the same team of Gujarat police and sought investigation by an SIT into the "cover-up".