A bench comprising justices Aftab Alam and Ranjana Prakash Desai perused the committee's report which said none of the six cases qualify as encounters and they are fake.
It said the security forces acted on source information and killed people without even cross-checking the information.
According to the bench, the report is distressing and the Centre should be more to blame than the state government for the situation in the northeastern state.
The committee, comprising former Supreme Court judge Santosh Hegde, ex-CEC J M Lyngdoh and a senior police officer, said in its report that the probe showed that none of the victims had any criminal records.
The bench said the report makes it clear that the guidelines on encounters laid down by the apex court in the Naga People's Movement case was not followed.
It said guidelines of apex court and NHRC were confined to papers and none of these were followed on the ground when armed forces and state police conduct operations.
Appropriate directions will be passed on the basis of the panel's report on April 9, it said while seeking response of the amicus curiae and NHRC on the recommendation made by the panel.
The bench also asked Additional Solicitor General Paras Kuhat to go through the report which was placed before it in a sealed cover.
On January 4, the Supreme Court had decided to appoint the committee to hold an inquiry into the alleged fake encounter killings in Manipur. The panel was set up to probe six cases of alleged extra-judicial killings in the state where a magisterial inquiry had raised questions on genuineness of the encounters.
The apex court had appointed the panel on a PIL filed by an association of the families of the alleged victims, seeking setting up of a special investigation team and direct inquiry into around 1,528 such cases.
The association had alleged in its plea that over 2,000 odd extra-judicial killings have taken place in the state, but no one has been held guilty till date.
It had alleged that innocent people with no criminal records have been killed by security forces and no proper investigation has been done in such cases.