"Thousands of men and boys have been detained by the Armed Forces - many have alleged torture, are held in secret places of detention and never seen again," the London-based rights watchdog said in its latest report.
Claiming that the region had deteriorated into a "legal wilderness", the report said that millions were locked in perpetual lawlessness in these tribal badlands with atrocities being committed both by armed forces as well as the Taliban.
"Detainees who are released alive and their families are threatened with dire consequences if they speak publicly about their treatment in detention," said the report, titled "The Hands of Cruelty: Abuses by Armed Forces and Taliban in Pakistan's Tribal Areas."
Although the Pakistan Armed Forces have wrested back control of most parts of the Tribal Areas from the Taliban over the past three years, they have arbitrarily detained thousands of individuals for long periods with little or no access to due process safeguards.
Human rights safeguards under Pakistan's constitution and the courts are excluded from the Tribal Areas, where the Armed Forces are using new broad security laws and a harsh colonial-era penal system to commit violations with impunity, the report said.