The apex court directed the CBI director to nominate a team of five officers for the SIT within two weeks, who will lodge the necessary FIRs and complete the investigation into the fake encounters by December 31 this year.
Calling upon states to adhere to the NHRC guidelines, the bench said "it is not as if the dignity of only living persons needs to be respected, even the dignity of the dead must be given due respect".
Directing the Centre and Manipur to extend full cooperation and assistance to the SIT without any "unnecessary hindrances or obstacles", the apex court asked the CBI chief to inform it about the composition of SIT in two weeks.
The court, which is hearing a PIL seeking probe into 1528 extra-judicial killings, ordered registration of FIR in 81 cases including 32 cases probed by a Commission of Enquiry, 32 cases investigated by judicial enquiries and high courts, 11 cases in which compensation has been awarded by NHRC and six cases probed by the commission headed by former Supreme Court judge Justice Santosh Hegde.
It had held that the use of "excessive force" by the armed forces or police was not permissible in 'disturbed areas' under the draconian AFSPA.
The apex court, which had directed a thorough probe into the alleged fake encounter killings, maintained that inquest was needed to "know the truth" in Manipur where "we need to be clear that the situation has never been one of a war or an external aggression or an armed rebellion that threatens the security of the country or a part thereof."
The bench today said that in none of the cases, FIR has been registered against the Manipur Police or any personnel of the central armed forces, while on the contrary, FIRs have been registered against the deceased for alleged violations of the law.
"Under these circumstances, it would be inappropriate for us to depend upon the Manipur Police to carry out an impartial investigation, more particularly when some of its own personnel are said to be involved in the fake encounters and the Manipur Police has not registered any FIR at the instance of the next of the kin of the deceased," it said.
"We cannot agree. Compensation has been awarded to the next of kin for the agony they have suffered and to enable them to immediately tide over their loss and for their rehabilitation," it said, adding that the step cannot override the law of the land, otherwise all heinous crimes would get settled through payment of monetary compensation.
"To suggest that all the inquiries were unfair and motivated is casting very serious aspersions on the independence of the authorities in Manipur at that point of time, which we do not think is at all warranted," the top court said.
It said if a crime has been committed, a crime which involves the death of a person who is possibly innocent, it cannot be overlooked only because of lapse of time.
The bench directed the listing of petitions in the second week of January next year to ensure compliance with the directions for probe by CBI.
The court said that difficulties highlighted by NHRC clearly indicate that it has been unfortunately reduced to a "toothless tiger" and directed the Centre to "expeditiously and favourably" consider the requests of the commission as it would be difficult for it to work effectively.
"We do feel it imperative to bring it to the notice of all State Governments that it would be but a small step in the protection of life and liberty of every person in our country if a State Human Rights Commission is constituted at the earliest," it said, adding that if the people are deprived of human rights or cannot have them enforced, "democracy itself would be in peril".
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