In a new report, the campaigning rights group says people are being terrorised by both the Taliban and the military.
It claims that abuses are allowed to take place with impunity as constitutional safeguards do not apply.
Militants have been driven out from some of the tribal areas but these districts are not yet fully secure.
“After a decade of violence, strife and conflict, tribal communities are still being subjected to attack, abduction and intimidation, rather than being protected,” said Amnesty International’s Polly Truscott.
The report, entitled The Hands of Cruelty, describes how what it calls the region’s “legal wilderness” is fuelling a human rights crisis.
It details cases where men and boys have been arbitrarily detained by armed forces for long periods with little or no access to due process or proper safeguards, as well as documenting multiple cases of deaths in custody.
Many of those detained have made allegations of torture, claims which have rarely investigated, it says.
Amnesty says that, because constitutional safeguards are not applicable to the tribal areas, armed forces are using broad new security laws to commit violations with impunity.
“By enabling the armed forces to commit abuses unchecked, the Pakistani authorities have given them free rein to carry out torture and enforced disappearance,” Ms Truscott said.
Locals describe living in fear of being tortured and killed by the Taliban if they are accused of being a spy, or of being picked up by the army accused of links to militants.
Amnesty is urging the Pakistani government to reform the legal system in the tribal areas which, it says, is perpetuating the cycle of violence.