THE FIGHT: Shi'ite fighters battling Islamic State militants in northern Tikrit in March claim a patch of ground. The Shi'ite militias, backed by Iran and under the nominal control of Baghdad, have been pivotal in the fight against Islamic State. REUTERS/Stringer

Rise of the militias

Torture by Iraqi militias: the report Washington did not want you to see

Two unpublished investigations show that the United States has consistently overlooked killings and torture by Iraqi government-sponsored Shi'ite militias.

ERBIL, Iraq – It was one of the most shocking events in one of the most brutal periods in Iraq’s history. In late 2005, two years after the U.S.-led invasion toppled Saddam Hussein, U.S. soldiers raided a police building in Baghdad and found 168 prisoners in horrific conditions.

Many were malnourished. Some had been beaten.

The discovery of the secret prison exposed a world of kidnappings and assassinations. Behind these operations was an unofficial Interior Ministry organisation called the Special Investigations Directorate, according to U.S. and Iraqi security officials at the time.

The body was run by militia commanders from the Badr Organisation, a pro-Iran, Shi’ite political movement that today plays a major role in Baghdad’s war against Islamic State, the Sunni militant group.

Washington pressured the Iraqi government to investigate the prison. But the findings of Baghdad’s investigation – a probe derided by some of its own committee members at the time as a whitewash – were never released.

The U.S. military conducted its own investigation. But rather than publish its findings, it chose to lobby Iraqi officials in quiet for fear of damaging Iraq’s fragile political setup, according to several current and former U.S. military officials and diplomats.

Both reports remain unpublished. Reuters has reviewed them, as well as other U.S. documents from the past decade.

The documents show how Washington, seeking to defeat Sunni jihadists and stabilise Iraq, has consistently overlooked excesses by Shi’ite militias sponsored by the Iraqi government. The administrations of George W. Bush and Barack Obama have both worked with Badr and its powerful leader, Hadi al-Amiri, whom many Sunnis continue to accuse of human rights abuses.

Washington’s policy of expediency has achieved some of its short-term aims. But in allowing the Shi’ite militias to run amok against their Sunni foes, Washington has fueled the Shia-Sunni sectarian divide that is tearing Iraq apart.

The decade-old U.S. investigation of the secret prison implicates officials and political groups in a wave of sectarian killings that helped ignite a civil war. It also draws worrying parallels to the U.S. government’s muted response today to alleged abuses committed in the name of fighting Islamic State.

Those accused of running the secret prison or of helping cover up its existence include the current head of the Iraqi judiciary, Midhat Mahmoud, Transport Minister, Bayan Jabr, and a long revered Badr commander popularly referred to as Engineer Ahmed.

“Special Investigations Directorate personnel illegally detained, tortured and murdered Iraqi citizens,” the U.S. report states. “Iraqi government officials failed to take action to stop the crimes.”

EVIDENCE: Abdul Salam al-Kubaisi, from Iraq’s Association of Muslim Scholars, shows a photo of a body found in a secret Baghdad prison in 2005. REUTERS/Thaier al-Sudani

“We do not violate the human rights.”

Muen Kadhimi, the Badr Organisation

The report says U.S. investigators faced a “lack of government cooperation, reluctance of witnesses to come forward and the perception of official complicity.”

Judge Mahmoud declined to comment for this story. A former colleague close to him said Mahmoud knew about the secret prison’s existence but did not know what went on there: “He cannot be held responsible for every judge’s behaviour.”

Transport Minister Jabr did not respond to Reuters’ queries. Jabr has previously stated publicly that no wrongdoing occurred at the prison.

A senior Badr official told Reuters that the prison allegations were part of a smear campaign by terrorists. He called for the international media to focus on Islamic State, which has carried out suicide bombings and executed prisoners.

U.S. officials acknowledge the role that Shi’ite militias such as Badr play in fighting Islamic State. As the Hashid Shaabi, or Popular Mobilisation Forces, the militias helped Baghdad defend the country against the Sunni jihadist group when Iraqi military and police divisions deserted en masse in 2014.

Since then, the militias have continued to attack Islamic State, which has declared a Caliphate across swathes of Iraq and Syria. Islamic State, also known as Daesh, routinely executes citizens who speak against it, kidnaps people, buys and sells women and children, and uses rape as a weapon.

American ambassador Stuart Jones told Iraqi state television in April this year “that the Hashid Shaabi is part of the Iraqi fighting forces which are defeating Daesh today.”

But Sunnis in areas freed from Islamic State control say the Shi’ite militias have been guilty of their own excesses, including looting, abductions and murder. At least 718 Sunnis in Salahuddin province have been abducted by fighters from Shi’ite militias since April 2015, according to several security officers, a provincial council member and tribal leaders. Only 289 have been freed, most after paying ransoms.

Some former and current U.S. officials say Washington needs to stop downplaying abuses by the Shi’ite militias.

Robert Ford, a former U.S. diplomat who served as the U.S. embassy’s political officer between 2004 and 2006, believes the U.S. government’s decision not to punish those behind the secret prison set a damaging precedent. “A few people were transferred elsewhere,” he said. “That’s not a punishment. You are supposed to scare them into not doing it.”

Ten years ago, Ford said, the militias were armed groups with political agendas, or the armed wings of political factions. “Now … the Prime Minister’s office has called them an official institution, and they receive resources directly from the state as well as a degree of political legitimacy.”

A Badr official, Muen al-Kadhimi, dismissed recent allegations of kidnapping, looting and killing. “We do not violate the human rights and we should not forget the inhumane ways practised by the enemy of the Iraqi people,” Kadhimi told Reuters.

NAMED: Bayan Jabr, former Iraqi interior minister, attends a parliamentary session in July 2014. REUTERS/Thaier al-Sudani

The Iraqi government conceded there has been a problem with kidnapping around Iraq, even in Baghdad, sometimes by men in security uniforms. “The Iraqi government is working hard to fight this,” said Saad Hadithi, a spokesman for Prime Minister Haider al-Abadi. He blamed “gangs” for the attacks, but said the state had “no concrete evidence of who is behind it.”

The U.S. embassy in Iraq and the State Department’s new counter-terrorism envoy, Brett McGurk, did not respond to requests for comment.


The Badr group spent years in exile in Iran. Its parent organisation, the Supreme Council for the Islamic Revolution in Iraq (ISCI), was the most powerful Shi’ite political force in Iraq.

After Saddam’s fall, Washington hoped ISCI and Badr would be reliable partners for the security forces, which Badr members joined in large numbers. But despite claims that they had demobilised after their return to Iraq, Badr’s fighters did not disarm, U.S. army intelligence officers say. Instead, they began to assassinate former Iraqi officers, influential Baath party members and civil servants.

Colonel Derek Harvey, a retired intelligence officer, told Reuters that the U.S. military detained Badr assassination teams possessing target lists of Sunni officers and pilots in 2003 and 2004 but did not hold them. Harvey said his superiors told him that “this stuff had to play itself out” – implying that revenge attacks by returning Shi’ite groups were to be expected. He also said Badr and ISCI offered intelligence and advice to U.S. officials on how to navigate Iraqi politics.

After Shi’ite religious parties swept to victory in elections in 2005, Badr and ISCI were given control of the Interior Ministry. The U.S. embassy publicly backed the move. But James Jeffrey, the top U.S. diplomat at the time and later ambassador to Iraq, was alarmed when Bayan Jabr, a Badr ally, became minister. “Bayan Jabr was the biggest mistake I made,” Jeffrey told Reuters. “His file was terrible.”

Jabr appointed Badr members to senior Interior Ministry posts. They created the covert Special Intelligence Directorate, which current and former U.S. officials believe coordinated the killing of former Saddam-era officials. Within months, Sunni politicians reported a sharp increase in the abduction of Sunni men. Some Sunnis blamed men in police uniforms. Corpses began to turn up around Baghdad.

LEADERS: (From left) General George Casey in November 2005. Casey was then the top U.S. military commander in Iraq; In December 2011, then U.S. Ambassador to Iraq James Jeffrey (far left), stood with U.S. Vice President Joe Biden, then Iraqi President Jalal Talabani and then Prime Minister Nuri al-Maliki, in Baghdad, to mark the end of American military presence in the country; U.S. President George W. Bush with then Ambassador to Iraq Ryan Crocker in Washington in February 2007. REUTERS/David Furst; Khalid Mohammed; Kevin Lamarque

The violence raised tensions between the U.S. military and officials in the U.S. embassy. Diplomats wanted those behind the killings brought to justice. Military officials were more prepared to turn a blind eye.

One U.S. diplomat said senior staff from the Iraqi security forces training command – then run by General David Petraeus – refused a U.S. embassy request for information on Iraqi troop movements in areas where Sunnis had been kidnapped. The diplomat said a senior staffer from the command told him privately: “At least they (the Iraqi security services) are getting the right guys.”

Petraeus told Reuters this month he had been concerned about the abuses and raised the issue with the Iraqi government and General George Casey, then head of the U.S. military in Iraq. Petraeus said that at the time the “responses were inadequate, in my assessment.”

Casey said the U.S. military set up a unit to monitor sectarian violence the month Petraeus left. “We leaned hard on our advisers … to provide actionable evidence,” Casey said. “Easier said than done. We had a very difficult time finding a smoking gun.”

According to Ford, General Martin Dempsey, who succeeded Petraeus, ordered his officers not to talk with U.S. diplomats about Iraqi security forces’ involvement in the killings.

Dempsey declined to comment.

Casey said his officers did their best “to prevent, stop and report any illegal or immoral acts by Iraqi forces.”

“Theoretically we could have punished someone.”

Zalmay Khalilzad, former U.S. Ambassador


Tensions exploded into the open in November 2005 when U.S. General Karl Horst, operations officer in Baghdad, received a tip that a missing Sunni teenager was being held in a secret Interior Ministry prison.

Horst raided the police building, in the Baghdad neighbourhood of Jadriya. The troops did not find the teenager but discovered the 168 detainees.

Washington faced a problem. The U.S. military in Iraq was battling Sunni radicals and the Shi’ite Mahdi Army movement. Badr was one of the few Iraqi forces not actively opposed to the Americans. But now, with what had become known as the Jadriya bunker, the militia had been directly linked to the bloodshed tearing Iraq apart.

U.S. officials pushed the Iraqis to investigate and submitted evidence directly to Ibrahim al-Jaafari, the prime minister. “‘He said there was nothing he could do,” Ford said.

Pressed by the Americans, Jaafari created an investigative committee. Its findings were never released. Jaafari, now Iraq’s foreign minister, did not respond to requests for comment.

The committee’s report, reviewed by Reuters, absolves the country’s security services and all government officials. Instead the Iraqi investigative committee said “Baathist” police had treated the prisoners badly.

Disappointed, Casey launched his own probe. The findings of that investigation, led by a U.S. military intelligence taskforce, were submitted to Casey in February 2006.

The U.S. report implicates Interior Minister Jabr and the Iraqi chief justice, Mahmoud. It also blames two men who ran the prison: Badr’s intelligence chief at the time, Bashar Wandi, who went by the name Engineer Ahmed; and a second Badr official, Brigadier General Ali Sadiq.

According to the U.S. report, Jabr was "complicit" and "indirectly responsible for illegal detentions, abuse, torture and extra-judicial killings." It said he had "failed to act on multiple reports of abuse and torture in the bunker" and called his conduct “an act of omission.”

POWER: Head of the Badr Organisation Hadi al-Amiri looks over military plans in Anbar province in May this year. REUTERS/Stringer

The U.S. military report states Mahmoud “was briefed regarding problems” at the prison by some of his judges and “took no steps to correct them.”

Mahmoud’s cooperation with the prison’s security officials “was required to assign judges who would ignore the rights of detainees, making him complicit,” the report says.

Despite calls from anti-corruption protesters in Baghdad for Mahmoud to be fired, the judge remains in post. In 2010, his office assigned investigative judges to interrogate detainees in another secret Baghdad prison. This second prison was run by the office of then Prime Minister Nuri al-Maliki and held more than 400 Sunni men from the city of Mosul. Some of the judges were implicated in torturing the detainees.

The U.S. report said Engineer Ahmed “had knowledge” of “illegal detentions, abuse and torture and concealed them from others.” His deputy, Ali Sadiq, was “directly responsible for illegal detentions, abuse, torture and extra-judicial killings.”

A separate internal U.S. military biography of Engineer Ahmed, produced later, said he answered directly to Hadi al-Amiri, the Badr boss. The biography called Ahmed “one of the most dangerous men in Iraq,” who led the “cruelest and most dangerous armed groups of the Badr Brigade while using … equipment, cars and uniforms from the Interior Ministry.”

Ahmed retained his position in the Interior Ministry for 18 months after the prison episode. The Badr organisation says he retired five years ago. But a U.S. military official and a former Iraqi security official say he continues to be in charge of Badr’s intelligence operations. An Iraqi lawmaker described him as high-ranking in Badr.

Reuters was unable to reach Ahmed or Ali Sadiq. Badr chief Amiri did not respond to requests for comment.

Badr official Kadhimi blamed the prison controversy on Sunnis opposed to the Shi’ite government. “The terrorists initiated this slander campaign,” he said.


In February 2006, days after General Casey received the U.S. military’s investigation of the first prison, Sunni militants blew up a Shi’ite shrine in Samarra. The attack triggered a full-scale civil war. Casey delivered the report to Jaafari, but said the prime minister, who was fighting to stay in office after national elections a few months earlier, had “no incentive to act” and resisted pressure.

“Our short-term solution is creating a greater long-term problem.”

Ryan Crocker, former U.S. ambassador

“Theoretically we could have punished someone, but the judgment was, ‘Let’s push the (Iraqi) government to do it,’” said Zalmay Khalilzad, U.S. ambassador at the time. “When the government failed to, we pushed for a change in the leadership.”

When Iraq’s new government was formed in May 2006, Jaafari was removed as prime minister and Jabr became finance minister. Khalilzad said the changes halted the growth of the Shi’ite militias’ influence inside the police, and the U.S. military started taking the worst national police units off the streets for retraining.

But other diplomats, Iraqi officials and U.S. military officers say the militias were so deeply embedded in the police and army that extra-judicial killings carried on until late 2007 and only faded out following an intensive U.S. troop build-up led by Petraeus, who had returned to Iraq earlier that year as the U.S. commander.

The people who paid the ultimate price were the secret prison’s detainees. A former Iraqi official told Reuters that at least 10 prisoners were killed following their release. One bunker survivor still fears for his security. He does not believe any lessons were learned from the episode. “The militias play free,” he told Reuters.

As the militias have played a growing role defending Iraq against Islamic State, their popularity has surged among the country’s Shi’ite population.

Americans have also applauded the Shi’ite paramilitaries victories. Jeffrey, the former ambassador who has now retired, said he did not worry last year when Islamic State swept across Sunni areas because he was confident that the Kurds and Amiri, the Badr boss, would join the battle. "(Amiri) is a radical revolutionary bloodthirsty killer,” Jeffrey said. “I like people who fight.”

In October, counter-terrorism envoy McGurk tweeted his congratulations to the Iraqi security forces and the militias after they seized the town of Baiji and its oil refinery from Islamic State.

In private, though, some U.S. military officers raise concerns. One senior U.S. military officer said he worries that the militias now control entire provinces. “Without real reconciliation, the Sunnis will stay angry and Islamic State will continue to gain support,” he said.

Ryan Crocker, who was U.S. ambassador in Iraq in 2007 at the height of the civil war, believes Amiri and his peers are now more powerful than the Iraqi military. “The more they assert themselves on the battlefield, the more they become the real power in the land, and the weaker Prime Minister Abadi gets,” Crocker said.

 Washington’s strategy of air strikes against Islamic State combined with turning a blind eye to Shi’ite excesses is cementing the militias’ power and helping break Iraq into its religious and ethnic parts, he said. "Our short-term solution is creating a greater long-term problem.”

AFTERMATH: The Golden Mosque, one of Iraq’s most important Shi'ite shrines, after it was bombed in February 2006. The attack pushed Iraq into civil war and prompted American officials to suppress a report into Shi’ite atrocities. REUTERS/Stringer


The War for Iraq

By Ned Parker

Photo editing: Simon Newman

Design: Catherine Tai

Edited by Simon Robinson