13 October 2014Last updated at 19:20 ET
The killings were in apparent revenge for attacks by Islamic State (IS).
Amnesty said the militias had been supported and armed by the Iraqi government and operated with impunity.
Prime Minister Haider al-Abadi, who took office last month, has admitted to previous "excesses" by security forces and vowed to govern for all Iraqis.
He has not yet commented directly on allegations contained in the Amnesty report but has previously said Iraq faces an "existential" battle against militants from Islamic State, also known as Isis or Isil.
Mr Abadi has also acknowledged, in what is believed to be a reference to Sunnis, that his government must address the "legitimate grievances" of the Iraqi people.
Yazidis enslaved The accusations against Shia militias in Iraq come two days after IS confirmed, in the latest issue of its propaganda magazine Dabiq, that it had captured and enslaved women and children from the Yazidi minority.
It said the women and children were seized around the town of Sinjar in northern Iraq and "were then divided according to the Sharia amongst the fighters of the Islamic State who participated in the... operations".
Some of the women were subsequently "sold", the magazine said.
The Amnesty report, based on interviews conducted in Iraq in August and September, provides details of what it says were sectarian attacks carried out by militiamen in the cities of Baghdad, Samarra and Kirkuk.
It says scores of unidentified bodies have been found, many still handcuffed and with gunshot wounds to the head, suggesting execution-style killings. Many others who disappeared remain unaccounted for.
Amnesty says that in Samarra, a mainly Sunni city north of Baghdad, it obtained details of more than 170 Sunni men abducted since June.
More than 30 were taken from or near their homes in a single day - 6 June - shot dead and their bodies dumped nearby.
"The killing spree seems to have been in reprisal for a brief incursion into the city the previous day" by IS fighters, Amnesty says.
'Blind revenge' Amnesty says the militias - including Asa'ib Ahl al-Haq, the Badr Brigades, the Mahdi Army and Kata'ib Hizbullah - have become more powerful since June, when the Iraqi army fell into disarray in the face of IS advances.
Correspondents say much of the fighting against IS since then has been carried out by militias, who were able to recruit thousands of volunteers, rather than the army.
There are now "tens of thousands" of militiamen, who "wear military uniforms but operate outside any legal framework and without any official oversight", Amnesty says.
The report quotes an unidentified Iraqi government official as saying that militias "mostly... kidnap Sunnis, because the victims can easily be labelled as terrorists and nobody is going to do anything about it".
Another unnamed government official said some Sunni men were considered to be "terrorists or terrorist supporters" because of where they lived. Others were killed "in blind revenge".
"I'm afraid that we're regressing back to the situation as it was seven or eight years ago, when this behaviour was very widespread," he said.
Militiamen have also tried to extort ransoms, sometimes killing their captives even after payments have been made, Amnesty said.
"I begged friends and acquaintances to lend me the ransom money to save my son but after I paid they killed him and now I have no way to pay back the money I borrowed, as my son was the only one working in the family," one mother said.
Amnesty says the militias have taken advantage of an "atmosphere of lawlessness" but the Iraqi government, which has armed and supported them, bears responsibility for their actions.
"By granting its blessing to militias who routinely commit such abhorrent abuses, the Iraqi government is sanctioning war crimes and fuelling a dangerous cycle of sectarian violence," said Amnesty's senior crisis response adviser, Donatella Rovera.
"The new Iraqi government... must act now to rein in the militias and establish the rule of law."
Shia militias 'killing Iraqi Sunnis in reprisal attacks'
Shia militias in Iraq have kidnapped and killed scores of Sunni civilians in recent months, a report by campaign group Amnesty International has said.
Amnesty said the militias had been supported and armed by the Iraqi government and operated with impunity.
Prime Minister Haider al-Abadi, who took office last month, has admitted to previous "excesses" by security forces and vowed to govern for all Iraqis.
He has not yet commented directly on allegations contained in the Amnesty report but has previously said Iraq faces an "existential" battle against militants from Islamic State, also known as Isis or Isil.
Mr Abadi has also acknowledged, in what is believed to be a reference to Sunnis, that his government must address the "legitimate grievances" of the Iraqi people.
Yazidis enslaved The accusations against Shia militias in Iraq come two days after IS confirmed, in the latest issue of its propaganda magazine Dabiq, that it had captured and enslaved women and children from the Yazidi minority.
It said the women and children were seized around the town of Sinjar in northern Iraq and "were then divided according to the Sharia amongst the fighters of the Islamic State who participated in the... operations".
Some of the women were subsequently "sold", the magazine said.
The Amnesty report, based on interviews conducted in Iraq in August and September, provides details of what it says were sectarian attacks carried out by militiamen in the cities of Baghdad, Samarra and Kirkuk.
It says scores of unidentified bodies have been found, many still handcuffed and with gunshot wounds to the head, suggesting execution-style killings. Many others who disappeared remain unaccounted for.
Amnesty says that in Samarra, a mainly Sunni city north of Baghdad, it obtained details of more than 170 Sunni men abducted since June.
More than 30 were taken from or near their homes in a single day - 6 June - shot dead and their bodies dumped nearby.
"The killing spree seems to have been in reprisal for a brief incursion into the city the previous day" by IS fighters, Amnesty says.
'Blind revenge' Amnesty says the militias - including Asa'ib Ahl al-Haq, the Badr Brigades, the Mahdi Army and Kata'ib Hizbullah - have become more powerful since June, when the Iraqi army fell into disarray in the face of IS advances.
Correspondents say much of the fighting against IS since then has been carried out by militias, who were able to recruit thousands of volunteers, rather than the army.
There are now "tens of thousands" of militiamen, who "wear military uniforms but operate outside any legal framework and without any official oversight", Amnesty says.
The report quotes an unidentified Iraqi government official as saying that militias "mostly... kidnap Sunnis, because the victims can easily be labelled as terrorists and nobody is going to do anything about it".
Another unnamed government official said some Sunni men were considered to be "terrorists or terrorist supporters" because of where they lived. Others were killed "in blind revenge".
"I'm afraid that we're regressing back to the situation as it was seven or eight years ago, when this behaviour was very widespread," he said.
Militiamen have also tried to extort ransoms, sometimes killing their captives even after payments have been made, Amnesty said.
"I begged friends and acquaintances to lend me the ransom money to save my son but after I paid they killed him and now I have no way to pay back the money I borrowed, as my son was the only one working in the family," one mother said.
Amnesty says the militias have taken advantage of an "atmosphere of lawlessness" but the Iraqi government, which has armed and supported them, bears responsibility for their actions.
"By granting its blessing to militias who routinely commit such abhorrent abuses, the Iraqi government is sanctioning war crimes and fuelling a dangerous cycle of sectarian violence," said Amnesty's senior crisis response adviser, Donatella Rovera.
"The new Iraqi government... must act now to rein in the militias and establish the rule of law."
From other news sites
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Daily Express RAF air strikes halt Jihadi advance in Iraq 5 hrs ago
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Telegraph Isil sells thousands of Yazidis as sex slaves 9 hrs ago
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London Evening Standard Hammond flies to Baghdad for talks on defeating Islamic State 10 hrs ago
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