The apex court said the special investigation team (SIT) should first complete the ongoing probe in 13 cases of the National Human Rights Commission (NHRC), followed by the matters related to judicial inquiry and those on which the high court had given its findings.
Thereafter, the SIT should take up the matters which were earlier dealt with by the a commission headed by former Supreme Court judge Justice Santosh Hegde and then the matters relating to commissions of inquiry should be probed, a bench comprising Justices Madan B Lokur and U U Lalit said.
"We have asked the Joint Director of the SIT (who is in charge) to expedite the cases related to NHRC," the bench said, adding "thereafter the SIT will look into the cases of judicial inquiries and high court followed by cases of the Justice Hegde commission and finally SIT will look into the commission of inquiry cases".
It also allowed CBI's plea to add five more officers in the SIT to probe these cases and asked Manipur's standing counsel to request the high court there to give the documents and records of the cases dealt with by it earlier to the SIT so that they could proceed with the investigation.
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Regarding the SIT's submission about delay in getting response from the central forensic science laboratory (CFSL), the bench asked its director to expedite the process.
Additional Solicitor General (ASG) Maninder Singh, who was appearing for the CBI, told the bench that progress has been made by the SIT in the ongoing probe in these cases.
He said there was a problem regarding interpreters since there were various languages in Manipur and SIT officials were having difficulty in recording the statements of witnesses there. He said some policemen from Manipur were sent to interpret the language.
The ASG also told the bench that SIT has found the whereabouts and identity of all the security personnel whose names have figured in these matters and some of them have also been examined during the probe.
He said that witnesses related to these cases were being examined by the SIT and each official has been assigned with investigation of two cases.
When the counsel appearing for one of the petitioners raised the issue of lodging of FIRs related to cases of judicial inquiry and commission of inquiry, the bench observed that SIT has so far lodged 42 FIRs and were in the process of conducting the probe.
Senior advocate Colin Gonsalves, appearing for the petitioners, told the bench that the FIRs have been lodged against "unknown persons" despite the fact that names of Army and police personnel were there in the records.
The bench, however, said that not naming these officials in the FIRs does not mean that they have been given clean chit since probe into these cases were going on.
It had on January 16 pulled up the CBI's SIT for not registering the required number of FIRs as directed by it earlier.
The court, which is hearing a PIL seeking a probe into as many as 1,528 cases of extra-judicial killings in Manipur, had on July 14 last year constituted the SIT comprising five CBI officers and ordered registration of FIRs and probe into the alleged extra-judicial killings in Manipur.