US Secretary of State Marco Rubio Warns of Iraq Fragmentation Amid Disarmament Challenges

Prime Minister of Iraq Ali al-Zaidi (far left), US President Donald Trump (centre), and other world leaders attend a multilateral meeting of the Gulf Cooperation Council at the United Nations General Assembly, on September 22, 2026, in New York City, the United States [Chip Somodevilla/Getty Images via AFP]

US Secretary of State Marco Rubio has warned that Iraq faces the threat of “Balkanisation” unless its armed factions are successfully brought under state control. Speaking to reporters at the Palace Hotel in New York City on Wednesday on the sidelines of the United Nations General Assembly, Rubio noted he had met with Iraqi Prime Minister Ali al-Zaidi the previous night. Rubio stated that while Washington has no doubts regarding al-Zaidi's commitment to disarming Iraqi armed groups, the task remains a massive and complex challenge.

According to Rubio, at least three armed groups have disarmed and integrated into the national government, whereas at least one group has shown far less cooperation. Bringing all weaponry under state control would ensure that Iraq no longer contends with independent forces operating to fracture the country, he added.

What does ‘Balkanisation’ mean? The term refers to a nation breaking apart into smaller, rival entities, typically along ethnic or religious lines, originating from the fragmentation of the Balkans during the collapse of the Ottoman Empire in the early 20th century. While the term often describes fears of territorial division in Iraq, Burcu Ozcelik, a senior research fellow for Middle East Security at the Royal United Services Institute (RUSI), told Al Jazeera that Rubio was specifically highlighting “fractures within the Iraqi state system” caused by Iran-aligned armed groups. These factions operate as rivals while also serving as conduits for pro-Iranian regime interests through parallel economic channels, political influence, and oil smuggling networks, she explained.

Is Iraq at risk of breaking up? Analysts suggest that an immediate territorial breakup is unlikely, though views on the severity of Rubio's warning vary. Ozcelik noted that Rubio's use of “Balkanisation” points more toward Iraq struggling to establish a centralized, stable state capable of resisting Iranian interference rather than facing imminent partition. Zeidon Alkinani, a Middle East political analyst and founding director of the Arab Perspectives Institute, offered a more skeptical perspective, telling Al Jazeera that Rubio's statement could be interpreted as either a political pressure tactic to accelerate Baghdad's disarmament efforts or an indicator of the administration's limited grasp of the region.

Discussions in New York involved meetings with Prime Minister Ali al-Zaidi, where officials addressed political, economic, investment cooperation, and regional security. The timing coincides with the approaching departure of the remaining US troops from Iraq on September 30, with Rubio confirming that no discussions have taken place regarding an extension of that timeline.

Most of Iraq's armed groups operate under the Popular Mobilisation Forces (PMF), a predominantly Shia formation established to combat ISIL (ISIS). While the PMF was formally integrated into Iraq's security forces a decade ago, many factions retain independent command structures and strong ties to Iran. Groups such as Saraya al-Salam, Asaib Ahl al-Haq, and Kataib al-Imam Ali have made arrangements with Baghdad, though powerful Iran-aligned factions like Kataib Hezbollah and Harakat al-Nujaba have refused, asserting they will retain their resistance weapons.

Furthermore, these armed groups have factored into broader regional conflicts, with Kataib Hezbollah and Harakat al-Nujaba previously targeting US forces and Gulf states during the US-Israel war on Iran. Rubio also highlighted that recent strikes on regional energy infrastructure were likely conducted in part by Iran-backed militias within Iraq. Meanwhile, new US sanctions are impacting Iranian airline routes, with Baghdad halting certain flights while attempting to reroute others through Najaf.