According to the report, after the military operation in parts of the Swat valley three years ago, many militants have been arrested. Many of these have been held without being formally charged.
Of those arrested, some have reportedly died while in captivity.
The army, which handles detained militants, says only 20-30 of those detained have died in custody. All of them though, they claim, died of natural causes.
Swat army spokesman Colonel Arif told BBC Urdu that all of those who died had been provided with the best medical help.
In the absence of credible autopsy reports, the army's claim cannot be verified, and serves only to add to the suspicion that the deceased prisoners were instead victims of extra-judicial killings.
A July 2010 Human Rights Watch report had accused the army of carrying out 238 such extra-judicial killings since September 2009.
The BBC Urdu research estimates that the since 2008, between 3,000 and 4,000 men have been arrested in Swat and six other districts of the Malakand division on terrorism charges. Official figures have not yet been made available.
The army claims that the frequency of such deaths have significantly decreased. However, unofficial sources told BBC Urdu that custodial deaths continue, and have instead, increased.
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Pak army killing unarmed prisoners, nothing new here...