BAGHDAD — The stalled battle to retake the Iraqi city of Fallujah from ISIS has given way to another grim development: accusations of human rights abuses against fleeing refugees by pro-Iraqi government forces.

The largely Shia militia group officially known as Hashd al-Shaabi or Popular Mobilization Forces (PMF), headed by Abu Mahdi al-Muhandis, a U.S.-designated terrorist has, according to the United Nations, committed atrocities against Sunnis in two newly liberated areas of Saqlawiyah and Al-Karmah, are just kilometers from Fallujah city.

Two sources in Saqlawiyah, who asked to remain anonymous due to fear of their lives, have told The Daily Beast that hundreds of civilian residents of Saqlawiyah and Karma have been heavily tortured by the PMF. Five dead bodies have been uncovered, but there are an additional 200 to 300 civilians that have been taken by the PMF; their fates are unknown.

Sheikh Raad Salman, of the Anbar-based Sunni Dulaim tribe, one of Iraq’s largest, told The Daily Beast that the “300 civilians have been buried alive” by the PMF and “700 more people have been severely tortured.”

Some say number of the victims is much higher. Hamid Mutlag, a Sunni MP and deputy head of defense committee in the parliament, told The Daily Beast “more than 800 residents of a village in Saqlawiyah have been taken by the Hashd al-Shaabi and there are others that have been killed and tortured.”

Atrocities in Fallujah have been expected as PMF leaders have been threatening to “cut the head of the snake” and accusing residents of having been cooperative with the Islamic State.

Saadoon al-Shalan, the mayor of Fallujah, said that Shia militias have sustained “huge losses” in the battle against ISIS and have lashed out at fleeing civilians. But the PMF leadership has nevertheless given “reassurances that they will not enter Fallujah and remain in the periphery.”

Reassurances are not enough in Iraq. Sectarian hatred is now so entrenched in light of the fact that the militias leading the operations in Saqlawiyah and Karma are the Badr Organization, Kata'ib Hezbollah (or the Brigades of the Party of God) and Asa'ib Ahl al-Haq the (League of the Righteous). All are directly backed by Iran’s Revolutionary Guards Corps and are notorious among the Sunni minority population for carrying out extrajudicial killings, torture and ethnic cleansing.

One source, who also asked to remain anonymous, has told The Daily Beast that the PMF are, in fact, planning to infiltrate into Fallujah city in the uniforms belonging to Iraqi Federal Police, a state security arm under the purview of the Interior Ministry, which is controlled by the Badr Organization.

Walid Muhammedi, member of the Islamic Party in Fallujah, echoed these warnings. “Hashd al-Shaabi militias wear uniforms of governmental forces and kill civilians from Fallujah and Saqlawiyah,” Muhammedi said. The head of the Federal Police in Fallujah, he noted, is Brigadier General Raid Shakir who was formerly the head of Federal Police in the southern Iraqi city of Wasit before being appointed in his current position in March. Shakir is understood to to have a close relationship with two senior commanders of PMF, the aforementioned al-Muhandis and his superior, Badr Organization leader (and former Iraqi Transportation Minister) Hadi al-Amiri.

Despite mounting documentary depicting torture and killing in Saqlawiyah and Al-Karmah, Karim Nouri, a spokesperson of the PMF, denied that the militias have committed any human rights abuses. “Hashd al-Shasbi has not committed any atrocities, it’s the media’s enemy of Hashd that spurred such untrue rumors to manipulate the public opinion,” Nouri told The Daily Beast.

“We are five kilometers away from the city. We have liberated 32 villages including Saqlawiyah, al Sagir and Al-Karmah,” he added.

The silence of American officials in the anti-ISIS coalition as U.S. warplanes provide air cover for the Iraqi military assault on Fallujah has only furthered the sense of Sunni alienation.“The Americans know very well what is going on in Fallujah and how the militias are committing atrocities in governmental uniforms,” Hamid Mutlag, a member of the Islamic Party said. “The US ambassador [Stuart Jones] knows the atrocities of Hashd al-Shaabi but has done nothing. Instead, he congratulates them for their efforts.”

Fallujah’s story is one of the most volatile and violent in post-Saddam Iraq. It is one of the few cities that have showed an absolute refusal to submit to the U.S. occupation in 2003. In late 2013 and early 2014, in reaction to then-Prime Minister Nouri al-Maliki’s increasingly sectarian policies, Fallujah became the site of big anti-government demonstrations on Friday. As Maliki declined to accept Sunnis’ demands, the Anbar Military Council was formed in Fallujah, declaring itself opposed to both the central government and the Islamic State. But by mid-2014 the city fell to the jihadists, forcing the Council to either accept their rule or surrender to Baghdad. It opted for the former because the Islamic State was seen as the lesser of two evils.

As the ongoing operation to once again retake this locus of insurgency away from jihadists grows more bloody, Sunnis and Shia grow further apart from each other. Iraqi is arguably at the nadir of sectarian relations since Prime Minister Haider al-Abadi took over from Maliki. Many are now asking if Fallujah, the symbolic capital of “resistance” and bastion of Sunni nationalism, could become this sect’s equivalent to the blowing up of the al-Askari Mosque in Samarra, an event perpetrated by ISIS’s predecessor, al-Qaeda, in 2006 which drove drove the country into a gruesome civil war.

— With additional reporting by Salam Zaidan