Justice Riaz Ahmed Khan summoned ISI chief Lt Gen Zaheerul Islam to appear before the court next week with an affidavit pertaining to the custody of the missing person.
The court was hearing a petition filed by Parveen Bibi who alleged that her husband Mohammad Arif was picked up by the intelligence agency.
During proceedings, Bibi's attorney informed the court that Arif and two others were taken into ISI custody a few months ago.
The attorney said those taken into custody with Arif had been released a few days later, while he was still in ISI custody.
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While some are later released, most of them remain in custody of security forces for long.
Many tortured bodies of such missing persons have been found in various parts of the country.
The problem is more acute in the restive Balochistan province and tribal areas.
For the first time in Pakistan's history, Defence Minister Khwaja Asif had last week lodged an FIR against some army officials in a case involving illegal removal of 35 undeclared inmates from an internment centre in Malakand who have been listed as missing.