'These are not allies': The most potent force fighting ISIS in Iraq has been accused of torturing and executing civilians

The US has been leaning heavily on militias in its fight against ISIS in Iraq and Syria, and while these forces have proved very effective on the ground, some have been accused of committing atrocities akin to their enemies.

A new Human Rights Watch report details allegations of torture and abuse at the hands of Shia militias in Iraq, which have been instrumental in aiding Iraqi Security Forces in seizing territory back from ISIS (also known as the Islamic State, ISIL, or Daesh).

The organization has "received credible allegations of summary executions, beatings of unarmed men, enforced disappearances, and mutilation of corpses by government forces" that have been fighting on the outskirts of Fallujah to retake the city from ISIS, according to the report.

Here are some of the allegations from the report:

• Human Rights Watch interviewed witnesses to one alleged atrocity near Fallujah who said Shia militia fighters and federal police had "separated men from women, marched the men to where the troops' officers were, lined them up, and shot at least 17 of them, including one teenage boy."
• Another witness told the organization that he saw Shia militia fighters and federal police near Fallujah "fatally shoot civilians with white flags raised fleeing toward the government forces." He claims one fighter "told him his superior officer had ordered the shootings."
• Some men whom Shia militias had recently released from detention "showed signs of torture, including rape, burns, knife cuts, and bruising from beatings."

The abuse allegations, which have become widespread in Iraq, are deepening the very sectarian tensions that facilitated the rise of ISIS in the first place. ISIS is a Sunni terror group that markets itself as a protector of Sunni civilians who have become targets of Shia militias, which have the support of the Shia-dominated Iraqi government.

Iran, a Shia theocracy and ally of Iraq, also backs these militias as it attempts to extend its influence in the Middle East.

As the Human Rights Watch report makes clear, civilians often end up caught in the middle of this sectarian power struggle.

The Iraqi government, wanting to keep Iran happy, hasn't done much to reign in these militias. As a result, they often go unchecked, using their power to suppress Sunnis.

"It's a concerted effort [on behalf of the Shia militias] to punish the Sunni population for, in their minds, accepting ISIS or allowing ISIS," Michael Pregent, an adjunct fellow at the Hudson Institute and former US Army intelligence officer in Iraq, told Business Insider.

"But in reality [Sunnis] had nowhere to go. They couldn't call the police, they couldn't call the army."

And it doesn't help that Fallujah has historically been a stronghold for extremists in Iraq.

Phillip Smyth, a researcher at the University of Maryland who is a leading expert on Shia militias, told Business Insider that people in Fallujah "gave Americans problems" during the Iraq War, and "gave the Iraqi government problems," so the militias' solution to routing the extremists "is to just smash" everything.

The Human Rights Watch report notes a video posted online that shows a Shia commander telling a room full of fighters that "Fallujah had been a bastion of terrorism since 2004 and that no civilians or true Muslims were left inside the city."

Treating all civilians in Fallujah as ISIS sympathizers plays right into ISIS' hand. If civilians are targeted by the militias that are supposedly liberating them from terrorist control, they become even more likely to turn against the Iraqi government.

"If the US continues to support Iraqi units that integrate Shia militias into their operations, they're simply resetting the conditions that led to ISIS to begin with," Pregent said. "You're further entrenching Sunni distrust of their government … and the United States."

These Shia militias are no friend to the US, either.

"These are not allies," Pregent said. "Everybody keeps thinking that these militias are working on a friendly basis with the US. They still hate us as much as they hate ISIS."

Still, there aren't many good alternatives, and it might be too late for the Iraqi government to reign in the militias without facing blowback from Iran.

"There's very very little that can really be done in order to turn this ship and make this all go away," Smyth said. "The genie has now been let out of the bottle, so how do you react to that?"

Militias are now deeply entrenched in Iraq.

"These groups are extremely powerful," Smyth said. "They have sometimes tens of thousands of members, they're actively deployed in multiple battlefronts. And beyond that they have very strong backers, particularly Iran."

On top of that, the Iraqi Army has been depleted so much as a fighting force that they can't effectively take on ISIS without the help of these militias.

"When you really look at it from a government point of view, they are not on the strong end of this," Smyth said. "They also have to deal with these forces because they're the ones taking the battle to the Islamic State."

Despite the evidence of Shia militia abuses, they're unlikely to face much punishment. There's too much support for the militias in the Shia-dominated Iraqi government - these organizations have fully integrated themselves not just on the battlefield, but in Iraqi politics as well.

"I don't think anything is going to come of it because if [Iraqi Prime Minister Haider] al-Abadi opposes the militias, he's likely to be deposed. … He has to accept their role in these operations," Pregent said.

"He could come back and say 'a couple of guys were punished,' but we don't ever really see these groups punished."

And it's not just the militias - Shiites from these organizations have also permeated the Iraqi Security Forces and federal police, Smyth said.

"You're not going to get much done," Smyth said. "They are integrated into the system."