The apex court, which said it had given the probe to the CBI so the truth would come out, asked the National Human Rights Commission to depute three persons to associate with the Special Investigation Team to carry out investigations in 17 of the 42 cases lodged by the SIT.
The SIT told a bench comprising Justices Madan B Lokur and U U Lalit that they have registered 42 cases and investigations were going on in accordance with the court's direction.
"We wanted the CBI to investigate the matter so that you can find out the truth," the bench said.
"What kind of investigation is this?" it asked.
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CBI's DIG Sharad Aggarwal, who is in-charge of the SIT, said all these FIRs, lodged earlier by the Manipur police, have been re-registered by the probe team.
Singh, who initially told the bench that the status report was approved by the CBI director, said he would file an affidavit in this regard.
"Your next status report will have approval of the CBI director specifically," the bench said and posted the matter for further hearing on March 12.
It said three persons, to be deputed by the NHRC, would be associated with the SIT and the investigation should be carried out on a "priority basis".
At the outset, senior advocate Colin Gonsalves, appearing for the petitioners, argued that except two cases, the other FIRs have been lodged against victims who had died.
The bench asked the SIT about it and referred to reports of a commission of inquiry, another commission headed by former Supreme Court judge Justice Santosh Hegde, the NHRC and findings of the Gauhati High Court in these matters.
"The allegations are that some persons were killed in fake encounters due to excessive use of force. The commission of inquiry, Hegde commission, high court and NHRC said that there was excess use of force. The persons who have used that excessive force are the accused," the bench observed.
The CBI's DIG told the bench that FIRs were lodged in accordance with the court's direction and they would investigate the matter and file charge sheets before the competent court.
"You will have to examine and investigate all facets," the bench said.
It referred to the FIRs and investigation conducted by the SIT and observed, "We are again back to square one."
Gonsalves said that despite specific orders of the court, there was resistance on the part of the SIT in lodging FIRs.
The bench, while making it clear that it has confidence in the SIT, said, "CBI has not understood us correctly. Please correct it and do it immediately. Enough is enough".
"You have to proceed with the investigation in accordance with our judgement," the bench said, adding, "Our judgement is very clear. We do not want explanation. You just follow our judgement".
The apex court 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 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.
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