It observed the Parliament could be approached if there existed no law to deal with the missing persons case.
Raja Irshad, counsel for Inter-Services Intelligence and Military Intelligence said that the existing Parliament did not represent the will of the people.
Chief Justice Iftikhar Muhammad Chaudhry told him that the incumbent Parliament represented the will of the people and had passed the 20th Constitutional Amendment to resolve issues.
"If you take them (Parliamentarians) into confidence, they will facilitate you as well," the CJP remarked.
The SC expressed immense dismay over the failure of the counsel for the ISI and the MI to justify arrest of 11 persons outside Adiala jail Rawalpindi on 29th May 2010.
In response to a constitutional petition from the relatives of 11 persons, the two spy agencies produced seven persons before the court on February 13, 2012 whereas bodies of four were received by their relatives in Peshawar.
A three-member bench led by Chief Justice of Pakistan has been hearing the petition filed by Ms Rohifa, the mother of three out of the seven prisoners.
Rohifa received the body of one of her sons on January 26, 2012.
She breathed her last on February 14 after meeting her two surviving sons in the apex court's premises on February 13.
During the hearing, the Chief Justice observed that the replies of counsel for the ISI and the MI Raja Irshad were unsatisfactory, observing that the replies submitted to the bench did not identify the law under which civilians were picked up by the agencies and kept in detention for more than a year.