The court has taken up the case of 41 disappeared persons whose relatives are convinced they are in the hands of the secretive intelligence agencies.
Human rights groups say innocent people are being abducted in the name of the war on terror.
The campaign to trace them has grown to include more than 100 families across the country in the past few months.
The government's lawyers said they had traced and released 25 missing persons out of the list of 41, and were doing all they could to find the rest.
Government officials have denied all knowledge of the disappeared.
But under Supreme Court pressure, some of the missing have been found in army camps - held there without charge.
A representative of the families of the disappeared, Amna Janjua, challenged the official count.
Pakistan's courts have found and freed a few prisoners
She said that only 18 were free. And she said some of these had testified that they had seen other missing people in captivity.
"We have got witnesses, we have got people with us who have been recently released and were telling us that they have actually seen people who are still detained, but their whereabouts are not known," she said.
By now more than 100 families have joined the campaign to find their loved ones.
Human rights groups say hundreds of people have been picked up in violation of local and international law, initially in connection with what is called the "war on terrorism".
But they say domestic critics of the regime are also disappearing - journalists, and activists demanding autonomy in the south-western province of Balochistan.
There is a growing determination to find them, but it will be a tough battle.
Last month police broke up a rally by force when demonstrators tried to deliver a petition to army headquarters.
Güncelleme Tarihi: 20 Eylül 2018, 18:16