A bench of justices Aftab Alam and Ranjana Prakash Desai, however, said it would pass the formal order on Monday after getting assents from Hegde and Lyngdoh.
The commission will be holding enquiry in six cases where the magisterial inquiry raised question on the genuineness of the encounter and security forces had "unlawfully" killed people including a 12-year-old boy.
The court was hearing a PIL by an association of the families of the alleged victims, pleading with the apex court to set up a special investigation team and direct inquiry into around 1528 such cases.
The association said in all, over 2000 odd extra-judicial killings have taken place in the state, but no one has been held guilty till date.
It alleged innocent people with no criminal records have been killed by security forces and no proper investigation has been done in such cases. (MORE)