In its annual global human rights report, the London-based organisation said US authorities executed 46 people over the past year, despite doubts in several case about the defendants' guilt and questions in others over legal representation or mental impairment.
At the Guantanamo Bay detention center on a US naval base in Cuba, 174 men were still being held at the end of the year, "including three who had been convicted under a military commission system which failed to meet international fair trial standards," the report said.
"Scores of men remained in indefinite military detention in Guantanamo as President (Barack) Obama's one-year deadline for closure of the facility there came and went," it said.
"Military commission proceedings were conducted in a handful of cases, and the only Guantanamo detainee so far transferred to the US mainland for prosecution in a federal court was tried and convicted."
Additionally, the report said "hundreds" were being held at the US airbase in Bagram, Afghanistan, without due process and some were "subjected to torture or other ill-treatment, including prolonged isolation, sleep deprivation and exposure to extreme temperatures."
Amnesty said US authorities also "blocked efforts to secure accountability and remedy for crimes under international law committed against detainees previously subjected to the USA's secret detention and rendition programme."
It said there were questions about "crimes under international law of torture and enforced disappearance," under the CIA program where detainees were transferred from one state to another "by means that bypass judicial and administrative due process."
It also noted that former president George W. Bush acknowledged in his memoirs that "he had personally authorised 'enhanced interrogation techniques' for use by the CIA against detainees held in secret custody."
In other criticisms of the United States, Amnesty said "excessive force" by US law enforcement was a concern, with 45 people killed during the past year after being struck by police Tasers - 450 deaths since 2001.
"Most of the deceased were unarmed and did not appear to present a serious threat when they were shocked," it said.
Amnesty also expressed concern about an immigration law passed in Arizona which could allow police to demand proof of legal status, fearing it would increase "racial profiling."