A former aide to General David Petraeus warns that as the Pentagon prepares to send another 1,500 US troops to Iraq to help “destroy” the Islamic State fighters, there may be an even greater danger that forces face: Iranian-backed Shiite militias.

The power of these militias has been growing throughout the country this year after Iraqi security forces were unable to prevail – and in some cases shed their uniforms and ran – while battling Islamic State fighters.

The Shiite militias are well-trained, in many cases by Iranian military commanders, and battle-tested. During the height of the Iraq war, these militias were responsible for the deaths of hundreds of US troops.

While the Islamic State is a potent military foe, it has comparatively little support from Iraqis. But Shiite militias play upon the worst fears of Iraq's Sunni and Kurdish minorities – that the Shiite majority is ruthlessly consolidating power. Indeed, some analysts say Iraqi Sunnis tolerate the Islamic State because it is seen as a counterweight to the Shiite militias.

In that way, Shiite militias could present a thornier problem to the future of a unified Iraq than does the Islamic State, which is also known as ISIS.

Back in 2007, “when I was serving with Petraeus, I mentioned to him that although Al Qaeda in Iraq was the wolf closest to the shed, in the long run Shiite militias could be more dangerous to Iraqi sovereignty,” says retired Colonel Peter Mansoor.

“Not much has changed – Al Qaeda in Iraq has been replaced by ISIS as the wolf closest to the shed,” says Dr. Mansoor, who is now an associate professor of military history at Ohio State University.

This is a view seconded by a number of seasoned Iraq analysts.

“As significant as is the threat from the Islamic State – and it is very significant – the threat posed by Shiite militias may well prove to be the long-term threat to Iraq,” says a former senior US commander in Iraq, who spoke on condition of anonymity.

This is because the Islamic State “has nowhere near the roots, numbers, nor attraction” to the Sunni population of Iraq that Al Qaeda in Iraq did at the start of the surge of US forces into Iraq in early 2007, the former commander explains.

What’s more, as US trainers come in with more intelligence and air attack assets, the security forces can be expected to engage the lslamic State with “increasing success,” he predicts.

And so the most significant challenge for Iraq may come later, “when Shiite and Sunni militia – and in some cases, Kurdish Peshmerga – clash over who will control areas of mixed sectarian populations.”

Shiite militias have displaced Sunni families from such areas for years. But those tensions could escalate and multiply in the months ahead if Islamic State fighters are cleared from such mixed areas, he adds.

In order to destroy the Islamic State, it’s going to be vital “to get Sunni tribes once again to turn on ISIS as they turned on Al Qaeda in Iraq,” Mansoor says. “I don’t think they’ll do that if they see the hidden hand behind the Iraqi government are these Shiite militias that are very sectarian.”

This “hidden hand” – which includes Iranian influence and, in some cases, command-and-control of operations – is increasingly apparent in the Shiite militias, says Kimberly Kagan, founder and president of the Institute for the Study of War.

“They ... going to erode Iraq’s sovereignty by taking the command-and-control of the security forces out of the hands of Iraqi officials, and placing that command-and-control into the hands of Iran.”

She cites photographic evidence of Iraqi security force (ISF) command centers “in which there are ISF commanders and Iranian-backed Shiite militias all sitting over a map evaluating plans.”

This has some implications for US troops headed to Iraq next month to train Iraqi security forces. The troops headed to Iraq will likely be deployed north of Baghdad and in Anbar province, where US officials are pushing to establish an “Iraqi National Guard” that would be composed of Sunni tribesmen.

“We must focus on training the Sunni tribes that actually stand a chance of providing long-term security in Anbar province,” the Sunni-dominated area of western Iraq, she adds.

The problem is that the Iraqi government continues to show “a preference for mobilizing Shiite militias rather than using the national guard force and mobilizing Sunni tribal leaders,” Kagan says.

Get the Monitor Stories you care about delivered to your inbox. By signing up, you agree to our Privacy Policy

The new prime minister, Haider al-Abadi, who was elected to the job in August, has pledged to change not just tenor and tone, but the substance of politics.

“In the short time he’s been in office he has succeeded in the former,” Mansoor says. “It’s unclear whether he’ll succeed in the latter.”