The London-based rights group said the abuses, often revenge attacks directed at Sunnis suspected of being complicit with IS, must not be repeated as Iraqi forces advance on the jihadists' stronghold in Mosul.
"After escaping the horrors of war and tyranny of IS, Sunni Arabs in Iraq are facing brutal revenge attacks at the hands of militias and government forces, and are being punished for crimes committed by the group," said Philip Luther, Amnesty's Middle East research director.
Amnesty International said that abuses, often revenge attacks directed at Sunnis suspected of being complicit with IS, must not be repeated as Iraqi forces a...
"As the battle to retake Mosul gets underway, it is crucial that the Iraqi authorities take steps to ensure these appalling abuses do not happen again."
The claims were made in a new report based on interviews with more than 470 former detainees, witnesses and relatives of civilians who have been killed, detained or disappeared, as well as officials and activists.
It cites an incident in May in which at least 12 men and four boys from the Jumaila tribe, who fled al-Sijir, north of Fallujah, were executed after handing themselves over to men wearing military and federal police uniforms.
In June, militias seized 1,300 men and boys from the Mehemda tribe who fled Saqlawiya, northwest of Fallujah, and many were tortured before being handed over to local authorities.
Survivors told Amnesty they were beaten and deprived of food and water. One said he was told it was "payback for the Speicher massacre".
In 2014, up to 1,700 military recruits from Camp Speicher, near Tikrit, were captured and killed by IS and allied militants. In August, 36 men were hanged for the crime.
"Iraqi authorities, whose complicity and inaction in the face of widespread abuses have contributed to the current climate of impunity, must rein in militias and make clear that such serious violations will not be tolerated," said Luther.
"Failure to do so will allow a vicious cycle of abuse, repression and injustice to continue and raises serious fears about the safety of civilians still in Mosul."