Attorney General Munir Malik informed a three-judge bench headed by Chief Justice Iftikhar Chaudhry - which is hearing a case related to "missing persons" or those detained without charge by intelligence agencies - that one of the persons died in December 2012 and another in July.
Malik further told the court that Defence Minister Khwaja Asif had informed him about the deaths last night.
The Chief Justice said the deaths had made the case more complicated. When he inquired about the cause of death, the Additional Defence Secretary informed the bench that the two detainees died of natural causes.
The Chief Justice observed that Ataullah, Superintendent of an internment centre at Malakand in the country's northwest, had submitted a statement in Peshawar High Court two years ago that said the army had handed over 35 people to him but took them away later.
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In a related development, the Khyber-Pakhtunkhwa government said there are 43 detention centres in the province.
During an earlier hearing of the case, the Chief Justice had warned the Defence Minister (the post was then held by the prime minister) and the Defence Secretary to either produce the 35 missing persons or face the consequences.