A bench of Justices M B Lokur and U U Lalit asked the CBI director to appoint a team of officers to conduct the probe into the alleged killings.
The court was hearing a PIL seeking probe and compensation in the alleged 1,528 extra-judicial killings in Manipur from 2000 to 2012 by security forces and police.
On April 20, the Army had told the apex court that it cannot be subjected to FIRs for carrying out anti-militancy operations in insurgency-prone areas like Jammu and Kashmir and Manipur, while alleging local bias in judicial inquiries conducted against it in these regions, which have tarnished its image.
The bench had also pulled up the Manipur government for not taking action on such alleged fake encounters by armed forces and asked was it "not supposed to do anything".
The Army had told the court that the judicial probes conducted into alleged extra-judicial killing charges were "biased" and slanted against them due to local factors.
It had alleged that the district judges, who were locals, had conducted the judicial inquiries into the alleged killings and local factors came in the way of the probe reports which went against the armed forces.
The apex court had earlier asked the Centre to segregate the cases related to the armed forces from the list of 265 incidents of extra-judicial killings in Manipur.
The Centre had said that out of the 282 cases, which were referred to it for verification, 70 matters were found to be related to the Army and Assam Rifles, while the rest concerned the state police.
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