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

More than 700 Sunni men and boys still are 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. Shiite militias did not pull back from Fallujah, participated in looting there and now vow to defy any American effort to limit their role in coming operations against the Islamic State group.

All told, militia fighters killed at least 66 Sunni males and abused at least 1,500 others fleeing the Fallujah 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.

Newsletter signup for email alerts

The battle against Islamic State is the latest chapter in the conflict between Iraq's Shiite 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 Shiite 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 underway for months. Sunni leaders in Iraq and Western diplomats fear the Shiite 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.

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 Fallujah 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 10 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 Shiite militias had gone missing around Fallujah, 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 spokesman, 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.

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 Shiite militias, trained and armed by Tehran, emerged during the 2003-11 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 Shiite militias whose members receive government salaries. The major groups have government posts and parliament seats.

Their might also has 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 Shiite militias are known as the Hashid Shaabi, or Popular Mobilization Forces . 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 Fallujah 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.