WASHINGTON(Reuters) - Shi’ite militias in Iraq detained, tortured and abused far more Sunni civilians during the American-backed capture of the town of Falluja in June than U.S. officials have publicly acknowledged, Reuters has found.

An Iraqi Shi'ite fighter fires artillery during clashes with Islamic State militants near Falluja, Iraq, May 29, 2016. REUTERS/Staff/File Photo

More than 700 Sunni men and boys are still missing more than two months after the Islamic State stronghold fell. The abuses occurred despite U.S. efforts to restrict the militias’ role in the operation, including threatening to withdraw American air support, according to U.S. and Iraqi officials.

The U.S. efforts had little effect. Shi’ite militias did not pull back from Falluja, participated in looting there and now vow to defy any American effort to limit their role in coming operations against Islamic State.

All told, militia fighters killed at least 66 Sunni males and abused at least 1,500 others fleeing the Falluja area, according to interviews with more than 20 survivors, tribal leaders, Iraqi politicians and Western diplomats.

They said men were shot, beaten with rubber hoses and in several cases beheaded. Their accounts were supported by a Reuters review of an investigation by local Iraqi authorities and video testimony and photographs of survivors taken immediately after their release.

The battle against Islamic State is the latest chapter in the conflict between Iraq’s Shi’ite majority and Sunni minority, which was unleashed by the 2003 U.S.-led invasion. The war ended decades of Sunni rule under Saddam Hussein and brought to power a series of governments dominated by Shi’ite Islamist parties patronized by Iran.

Washington’s inability to restrain the sectarian violence is now a central concern for Obama administration officials as they move ahead with plans to help Iraqi forces retake the much larger city of Mosul, Islamic State’s Iraqi capital. Preliminary operations to clear areas outside the strategic city have been under way for months. Sunni leaders in Iraq and Western diplomats fear the Shi’ite militias might commit worse excesses in Mosul, the country’s second-largest city. Islamic State, the Sunni extremist group, seized the majority-Sunni city in June 2014.

“CENTRAL TOPIC”

U.S. officials say they fear a repeat of the militia abuses in Mosul could erase any chances of reconciling Iraq’s Sunni and Shia communities. “Virtually every conversation that we have had internally with respect to planning for Mosul - and virtually every conversation that we’ve had with the Iraqis - has this as a central topic,” said a senior Obama Administration official.

In public, as reports of the abuses in Falluja emerged from survivors, Iraqi officials and human rights groups, U.S. officials in Washington initially played down the scope of the problem and did not disclose the failed American effort to rein in the militias.

Brett McGurk, the special U.S. envoy for the American-led campaign against Islamic State, expressed concern to reporters at a June 10th White House briefing for reporters about what he called “reports of isolated atrocities” against fleeing Sunnis.

Three days before the briefing, Gov. Sohaib al-Rawi of Anbar Province informed the U.S. ambassador that hundreds of people detained by Shi’ite militias had gone missing around Falluja, the governor told Reuters. By the time of the White House briefing, Iraqi officials, human rights investigators and the United Nations had collected evidence of scores of executions, the torture of hundreds of men and teenagers, and the disappearance of more than 700 others.

Nearly three weeks later, on June 28, McGurk struck a measured tone during testimony to the Senate Foreign Relations Committee. He said reports of abuses had been received in the early days of the operation, “many of which have turned out not to be credible but some of which appear to be credible.”

McGurk declined a request for an interview. Mark Toner, the State Department’s deputy spokesperson, said American officials had expressed “concern both publicly and privately” about reported atrocities. “We find any abuse totally unacceptable,” Toner said, and “any violation of human rights should be investigated with those responsible held accountable.”

Militia leaders deny that their groups mistreated civilians. They say the missing men were Islamic State militants killed in battle.

EXACTING REVENGE

Iraqi government officials also challenged the reports of widespread violence against civilians. In an interview, Iraqi Prime Minister Haider Al Abadi’s deputy national security adviser, Safa al-Sheikh, said there were a few incidents, but added: “There are a lot of exaggerations, and some of the reports didn’t have any basis.”

Iraq’s main Shi’ite militias, trained and armed by Tehran, emerged during the 2003-2011 U.S. occupation and have grown in power and stature. After helping the government defend Baghdad when Islamic State seized Mosul in 2014, the militias became arms of the Iraqi government. Islamic State has slaughtered thousands of Iraqis, of all faiths.

There now are more than 30 Shi’ite militias whose members receive government salaries. The major groups have government posts and parliament seats.

Their might has also been enhanced by some of the more than $20 billion in military hardware the United States has sold or given to Iraq since 2005. Their weaponry includes armored personnel carriers, trucks, Humvees, artillery and even tanks, according to U.S. officials, independent experts and pictures and videos militia members have posted on the internet.

Collectively, the Shi’ite militias are known as the Hashid Shaabi, or Popular Mobilization Forces (PMF). The militias officially answer to Abadi. In reality, the main groups answer only to themselves, display their own flags and emblems, and are advised by the Quds Force - Iran’s elite foreign paramilitary and intelligence service.

The Falluja offensive began on May 22. For more than a year, American officials had warned Iraqi officials repeatedly that the United States would suspend air support in areas where militias were operating outside the Iraqi military’s formal chain of command. The policy was designed to prevent American planes from inadvertently bombing Iraqi forces and to restrain militias from entering areas considered sensitive to Sunnis, according to U.S. officials.

In the first two days of the Falluja offensive, reports emerged of militiamen separating males from fleeing families. American, Western and U.N. diplomats pressured Abadi, other top Iraqi officials and militia leaders to stop the abuses.

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Abadi and other political leaders publicly called for protection of civilians.

“DON’T BE TREACHEROUS”

The Americans’ influence was hindered by the fact they had no forces in Falluja and couldn’t observe specific abuses, according to the Western diplomat who tracked the campaign.

On May 26, Ayatollah Ali Sistani, Iraq’s leading Shi’ite cleric, pleaded with combatants to protect civilians. Aid agencies estimated at the time that as many as 100,000 people remained inside Falluja.

“Don’t be extreme ... don’t be treacherous. Don’t kill an old man, nor a boy, nor a woman. Don’t cut a tree unless you have to,” Sistani said, citing sayings of the Prophet Mohammed.

Sistani’s pleas and the American threats fell on deaf ears.

The first known instance of systematic abuse by the militias in the Falluja offensive occurred May 27 northeast of the city, in the farming region of Sejar. Militiamen and security forces stopped a group of fleeing Sunnis, pulled aside somewhere between 73 and 95 males aged 15 and older and took them away, according to Gov. al-Rawi of Anbar Province and a Western diplomat who monitored the offensive. Women and children were freed.

“We are still in contact with women and children who were handed to government people,” said the Western diplomat. “They still don’t know where the men are.”

On May 29, militiamen just west of the farming areas of Sejar, separated 20 men from a group of fleeing Sunnis and “started killing them,” said the Western diplomat. “The police arrived when there were three left alive. The police took the three and dumped them” in a camp east of Falluja for people displaced by the civil war.

Terrified that the militias would storm the camp and kill them, the trio arranged protection for themselves in Baghdad, the diplomat said. Gov. al-Rawi confirmed this account.

A Sunni academic said he spoke to three survivors of the alleged massacre, two brothers and their cousin. The men said the killings occurred during fighting between Iraqi federal police forces and Islamic State, according to the academic.

SURVIVOR ACCOUNTS

The three survivors told the academic that they were among some 50 people who had sought shelter in a house when they saw federal police raise the Iraqi flag at a nearby school. The group waved white cloths and was directed to leave the house by the police.

When the group emerged, the three said, the police separated the men from their families. One officer then opened fire and killed 17 men, the academic quoted the survivors as saying, adding that the three were spared when another officer intervened. The shooter was arrested, according to the Anbar governor.

Worse was to come. Shi’ite militiamen seeking vengeance against Islamic State rounded up Sunnis on June 3 from the town of Saqlawiya, according to witnesses interviewed by Reuters, U.N. workers, Iraqi officials and Human Rights Watch.

According to these accounts, more than 5,000 Sunnis, mostly members of the al-Mohamda tribe, left Saqlawiya, a farming community five miles northwest of Falluja. The Sunnis made their way toward what they thought was the safety of government lines marked by Iraqi flags. A gray-haired man described the scene in a video recorded by local officials after he and 604 other men were freed two days later.

“When we arrived there, we discovered they were the Hashid,” the Shi’ite militias, the witness said.

U.N. High Commissioner for Human Rights Zeid Raad al-Hussein, two senior Iraqi officials, and a 69-year-old survivor interviewed by Reuters identified the militiamen as members of Kataib Hezbollah. One of the most powerful Shi’ite paramilitaries, Kataib Hezbollah was organized by and retains close ties to Iran’s Quds Force. Both are deemed to be terrorist groups by the United States.

Kataib Hezbollah denied being involved in abuses in Falluja. “They make these claims based on accusations from politicians that ISIS is depending on,” said Kataib spokesman Jaafar al-Husseini. “They are trying to keep us far from the operations of Anbar and Mosul.”

The militiamen separated out an estimated 1,500 males aged 15 and older and moved them in groups to different locations, including warehouses and an Iraqi base called Camp Tariq, according to survivors, U.N. investigators and Human Rights Watch.

“FISTS, KNIVES AND CABLES”

The survivors described being crammed into small rooms and halls and denied food and water, straining to breathe in the stifling heat. Militiamen using sticks, pipes and hoses beat the detainees and declared that they were taking revenge for Camp Speicher – a June 2014 massacre by Islamic State of 1,566 Shi’ite and other non-Sunni air force cadets.

A 32-year-old man, one of six survivors Reuters interviewed, said he was packed into a room with dozens of other captives, his hands tied behind his back.

“They started hitting us with their fists, knives and cables,” he said. “When people fainted, we yelled they were going to die, and the guards told us that’s what they wanted.”

The guards, the survivor said, told the captives they were avenging the deaths of hundreds of Iraqi soldiers killed in fighting around Falluja since 2014.

In a video recorded by local officials, another survivor told how men craving water were given bottles in which to urinate and told to drink their own waste.

A 47-year-old survivor described how he watched militiamen repeatedly beat his 17-year-old son and carry off the corpses of 15 men who appeared to have been beaten to death. The man was one of the 605 survivors released on June 5. His son was not among them, he said; the boy hasn’t been seen since.

“We want to know the destiny of our sons,” the man told Reuters. “We consider the Americans responsible for everything that has happened.”

UNACCOUNTED FOR

In all, militiamen killed at least 49 men who were detained in Saqlawiya, four of whom were beheaded, according to the U.N.’s Zeid.

The brutality ended without explanation for some 800 detainees after two days. But 643 Saqlawiya detainees remain unaccounted for. Their names are recorded on a list circulated by local officials to the United Nations, Human Rights Watch and government investigators and reviewed by Reuters.

On June 7, Sheikh Ali Hamad, a leader of the Mohamda, a Sunni tribe, decried on television what he called “a genocidal crime” and the deaths of “tens of our sons.”

The same day, the Anbar governor informed U.S. Ambassador Jones that hundreds of Sunni men were missing. U.N. envoy Zeid issued a statement citing “extremely distressing, credible reports” of abuse, including summary executions of men and boys by militiamen.

On June 9, the day before McGurk’s White House briefing, Human Rights Watch issued a report on the alleged atrocities in Sejar and Saqlawiya.

The regular Iraqi security forces, including the U.S.-trained Counter-Terrorism Service, eventually established safe corridors and guided civilians out of the city. Some 100,000 civilians escaped as a result.

A PIECE OF THE ACTION

Today, the Shi’ite militias are clamoring to join the Mosul offensive, fired by zeal, a desire for revenge and hopes of burnishing their political standing within their sect.

“They will want a piece of the climactic battle,” said Kenneth Pollock, a former CIA analyst now with the Brookings Institution, a Washington policy institute.

Ryan Crocker, a career diplomat who served as U.S. ambassador to Iraq from 2007 to 2009, said the Obama administration has downplayed abuses by both militia and Iraqi forces. “This administration is so determined to be able to declare victory over ISIL (that) they don’t really care about any of the rest of it,” said Crocker.

Over the disapproval of the Mosul provincial government, Abadi and militia leaders have said that militias will participate in the campaign to liberate the city.

The chief PMF administrator is Jamal Ibrahimi. Known by the nom de guerre Abu Mahdi al-Mohandis, he is on the U.S. international terrorist list.

U.S. officials say Ibrahimi is the leader of Kataib Hezbollah, the militia that Iraqi officials, Western diplomats and others hold primarily responsible for the atrocities committed in the Falluja offensive.

Ibrahimi and the militia deny that he heads Kataib Hezbollah.

Abadi’s office has announced that a committee will investigate allegations of rights abuses in Falluja. It is uncertain if the inquiry will find anyone responsible beyond a handful of low-level suspects whose arrests Abadi reported on June 13.

(This version of the story has been refiled to remove word “new” from headline)