Reports say Shia militias in Iraq detained, tortured and abused far more Sunni civilians during the American-backed capture of the town of Fallujah in June than US officials have publicly acknowledged.

More than 700 Sunni men and boys are still missing more than two months after the Islamic State of Iraq and the Levant (ISIL) group stronghold fell, says Reuters news agency.

The abuses occurred despite US efforts to restrict the militias' role in the operation, including threatening to withdraw American air support, according to US and Iraqi officials.

The US efforts had little effect. The Shia militias did not pull back from Fallujah, participated in looting there, and now pledge to defy any American effort to limit their role in forthcoming operations against ISIL.

Do Shia militias stoke sectarian tension in Fallujah?

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.

The Shia militia leaders deny that their groups mistreated civilians.

They say the missing men were ISIL fighters killed in battle. Iraqi government officials also challenged the reports of widespread violence against civilians.

Iraq's main Shia militias, trained and armed by Iran, emerged during the 2003-2011 US occupation and have grown in power and stature.

After helping the government defend Baghdad when ISIL seized Mosul in 2014, the militias became arms of the Iraqi government.

Abuse records

In July, Human Rights Watch urged Iraqi military commanders to ban militias with abuse records from the fight to reclaim Mosul from ISIL.

The battle against ISIL is the latest chapter in the conflict between Iraq's Shia and Sunni communities, which took root after the 2003 US-led invasion.

The war ended decades of Sunni rule under Saddam Hussein and brought to power a series of governments dominated by Shia parties patronised by Iran.

US 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, ISIL’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 Shia militias might commit worse excesses in Mosul, the country’s second-largest city.

ISIL seized the Sunni-majority city in June 2014, and US 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 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, US 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 US envoy for the American-led campaign against ISIL, expressed concern to reporters at a June 10 White House briefing for reporters about what he called "reports of isolated atrocities" against fleeing Sunnis.

'Hundreds missing'

Three days before the briefing, Sohaib al-Rawi, governor of Anbar province, informed the US ambassador that hundreds of people detained by Shia militias had gone missing around Fallujah.

By the time of the White House briefing, Iraqi officials, human rights investigators and the UN 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 US 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. "Any violation of human rights should be investigated, with those responsible held accountable."