Volunteers with Iraq’s Badr Organization patrol in Tikrit, Iraq, on Feb. 7. Badr and other Iran-backed Shiite militias are playing a more important role in the fight against the Islamic State. (Ali Mohammed/European Pressphoto Agency)

Shiite militias backed by Iran are increasingly taking the lead in Iraq’s fight against the Islamic State, threatening to undermine U.S. strategies intended to bolster the central government, rebuild the Iraqi army and promote reconciliation with the country’s embittered Sunni minority.

With an estimated 100,000 to 120,000 armed men, the militias are rapidly eclipsing the depleted and demoralized Iraqi army, whose fighting strength has dwindled to about 48,000 troops since the government forces were routed in the northern city of Mosul last summer, according to U.S. and Iraqi officials.

A recent offensive against Islamic State militants in the province of Diyala led by the Badr Organization further reinforced the militias’ standing as the dominant military force across a swath of territory stretching from southern Iraq to Kirkuk in the north.

As they assume a greater role, the militias are sometimes resorting to tactics that risk further alienating Sunnis and sharpening the sectarian dimensions of the fight.

They are also entrenching Iran’s already substantial hold over Iraq in ways that may prove difficult to reverse. Backed and in some instances armed and funded by Iran, the militias openly proclaim allegiance to Tehran. Many of the groups, such as the powerful Asaib Ahl al-Haq and Kitaeb Hezbollah, are veterans of the fight to eject American troops in the years before their 2011 departure.

In one telling sign of how far Iraq is sliding into Iran’s orbit, giant billboards advertising the militias’ prowess and featuring portraits of Iran’s late Ayatollah Ruhollah Khomeini and his successor as supreme leader, Ayatollah Ali Khamenei, now partially obscure the plinth in central Baghdad where Saddam Hussein’s statue stood before U.S. Marines tore it down in 2003.

The militias’ growing clout is calling into question the sustainability of a strategy in which U.S. warplanes are bombing from the sky to advance the consolidation of power on the ground by groups that are backed by Iran and potentially hostile to the United States, analysts say.

If the fighting continues on its current trajectory, there is a real risk the United States will defeat the Islamic State but lose Iraq to Iran in the process, said Michael Knights of the Washington Institute for Near East Policy. Though Iraq’s Prime Minister Haider al-Abadi has welcomed American assistance and is calling for more, the militias’ strength threatens to undermine his authority and turn Iraq into a version of Lebanon, where a weak government is hostage to the whims of the powerful Hezbollah movement.

“The Shiite militias don’t want the Americans there and they never did,” Knights said. “Will we see an attempt by these Iranian-backed militias to push us out completely?”

As U.S. commanders mull sending ground troops to assist a planned offensive to retake Mosul, some militia groups are already starting to question the need for U.S. help.

“We don’t need them, either on the ground or in the air,” said Karim al-Nouri, spokesman and military commander for the Badr Organization, which has emerged as the most powerful of the armed groups. “We can defeat the Islamic State on our own.”

‘Exceptional methods’

Iraqi officials point out that militias have filled a huge need, providing muscle and manpower at a critical time and helping reverse the Islamic State’s advance toward Baghdad. U.S. help came late, more than two months after the militants surged toward the capital, they complain. An effort to rebuild the collapsed Iraqi army only began in December and so far has not graduated any trainees.

“We are in a transitional period, and we are in a state of emergency,” said Mowaffak al-Rubaie, a member of parliament with Abadi’s State of Law coalition. “There is an existential threat, and that threat warrants using exceptional methods.”

The militias, which prefer to be described as “popular mobilization forces,” point out that their deployment has been authorized both by the government and by a fatwa from Iraq’s chief religious authority, Grand Ayatollah Ali Sistani.

But the militias’ chain of command runs through their own leaders, and in many instances directly to Iran. The man appointed to coordinate their activities is Iraq’s deputy national security adviser, Abu Mahdi al-Muhandis, the nom de guerre of an Iraqi sanctioned by the U.S. Treasury for his role as a top Iraqi commander in Iran’s Revolutionary Guard Corps. He was convicted in absentia by Kuwait for his part in bombings at the U.S. and French embassies in Kuwait in 1983.

Qassem Soleimani, the top commander of the Iranian force, makes regular appearances on the front lines in Iraq, echoing the battlefield swings undertaken in the last decade by U.S. generals.

Direct battlefield command is increasingly being assumed by the newly powerful Badr leader Hadi al-Amiri, who claims to be responsible for drawing up war plans on behalf of the security forces as well as the militias.

At a rally held earlier this month to celebrate the rout of Islamic State fighters in the province of Diyala, Amiri took the starring role.

“Our mission is to liberate Iraq with Iraqis, and not with foreigners,” Amiri told jubilant fighters chanting his name. “We must fight sectarianism, bring reconciliation and maintain the unity of Iraq.”

Killings in a village

On a tour of the recently liberated villages, the danger that the militias’ role might only serve to enhance sectarianism was apparent. In one village, al-Askari, every home had been burned, a tactic Sunni politicians allege is intended to cleanse whole areas of Sunnis and prevent them from returning home.

Badr escorts declined to take reporters to another village, Barwana, where at least 53 and possibly as many as 70 Sunni men were found shot dead execution-style after the Islamic State defeat. Witnesses and Sunni politicians say the men were civilians who had taken refuge in Barwana after their own village was overrun by the militants. They accuse Shiite militias of carrying out the killings.

The Badr Organization has denied that it was involved, but its leaders also deny that the men were civilians.

“Those Barwana people who stayed belonged to the Islamic State,” said Nouri. “What were we to do? Throw roses to them, or kill them?”

“The Islamic State are savages,” he added. “When we face them, we expect mosques to fall down and houses to burn, because we are not playing a football match with them, and we are not having a picnic.”

‘Terrified’ Sunnis

Such methods will not help promote the reconciliation that forms a central plank of U.S. policies toward Iraq, said Kenneth Pollack of the Brookings Institution, who recently visited Baghdad and noted the surge in militia influence with alarm.

“The Iraqis are getting ready to reconquer the Sunni heartland, and they’re going to go in with a Shiite force,” he said. “The Sunni populace are terrified, and they will regard this as a Shiite invasion of their homeland. That won’t end the civil war, it will inflame it.”

Despite the militias’ boasts, however, it is unclear whether they are capable of pursuing the fight into the Sunni heartland, including the provinces of Anbar, Salahuddin and Nineveh, where the Islamic State is most firmly established.

So far their successes have been confined mostly to areas where Shiites predominate, including to the south of Baghdad, some parts of eastern Salahuddin and most recently, Diyala.

But Nouri, the Badr commander, said the militias would prefer not to have American help even for an assault on Mosul.

If the United States wants to continue with its airstrikes now, “we don’t have a problem,” he said. “But they should not strike while we are on the ground. We don’t want history to record that we conducted an offensive with American cover.”

Mustafa Salim contributed to this report.