The 70-page report "Hands of Cruelty" from Amnesty International says the Pakistani army operates outside internationally accepted laws governing human rights.
The Taliban also continues to punish government sympathizers in the federally administered Pakistani tribal areas bordering Afghanistan.
"After a decade of violence, strife and conflict, tribal communities still are being subjected to attack, abduction and intimidation rather than being protected," Amnesty International's Deputy Asia Pacific Director Polly Truscott said.
Amnesty International said human rights safeguards under Pakistan's Constitution and the courts are excluded from the tribal areas. The military uses new broad security laws and a harsh colonial-era penal system 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," said Truscott.
Meanwhile, the Taliban and other armed groups "pose a deadly threat to Pakistani society" by indiscriminately killing villagers and targeting others.
"The Taliban have time and again shown complete disregard for civilian lives by these indiscriminate and deliberate attacks," Truscott said.
They also carry out brutal killings of captured soldiers and suspected spies, often dumping their bodies as a warning to others.
The report said research found "39 cases of enforced disappearance carried out by the armed forces in the Tribal Areas and is concerned that these represent only a fraction of the total."
But the Pakistani military rejected the document, calling it "a pack of lies," a report by the BBC said.
An army spokesman told the BBC the Amnesty International report was "biased and sinister propaganda" against the military and based on fabricated stories.
The report is based on research conducted by Amnesty International in late 2011 and in March, July and August this year.
Amnesty International said it analyzed government and legal documents relating to thousands of individuals detained under the Actions (in Aid of Civil Power) Regulations 2011 and several others detained under the Frontier Crimes Regulation.
Amnesty International also considered testimony from people in detention, witnesses, relatives, lawyers and representatives of Pakistani authorities and armed groups.
Truscott called for the government immediately to reform "the deeply flawed legal system in the tribal areas that perpetuates the cycle of violence."
Pakistan's military has been fighting the main rebel groups Tehrik-i-Taliban Pakistan and Lashkar-e-Islam, since 2004 at the start of the army's search for al-Qaida fighters.
While the fighting was initiated in the name of Pakistan's part in the war on international terrorism, accusations of human rights abuses have become prevalent.
The tribal areas also are subject to intense U.S. drone attacks targeting suspected al-Qaida bases and groups.
Earlier this month, senior al-Qaida leader known as Abu-Zaid al-Kuwaiti was killed in a drone strike as he ate breakfast, an Islamist website said.
U.S. officials confirmed the news, NBC News reported. Experts said Sheik Khalid Bin Abdul Rehman Al-Hussainan was one of the top remaining leaders of al-Qaida following the death of Osama bin Laden in a U.S. attack inside Pakistan.
Hussainan as believed to be a possible successor to Ayman al-Zawahiri, bin Laden's deputy and successor.
Hussainan was the highest-ranking al-Qaida official to be killed by the United States since Anwar al-Awlaki in September 2011. Awlaki, a U.S. citizen, died in a drone strike in Yemen.