BAGHDAD — The top U.S. general in Iraq says the fallout from last month’s Kurdish vote for independence is diverting resources away from the war on the Islamic State group just as the coalition is on the verge of defeating the extremists.

U.S.-backed Iraqi and Kurdish forces, who together have driven IS out of most of the country, are locked in an increasingly tense standoff. Low-level clashes have broken out as federal forces have driven the Kurds from disputed areas, and on Thursday Iraq’s prime minister rejected a Kurdish offer to “freeze” the referendum, an apparent attempt by the Kurds to save face.

“We don’t need Iraqis killing Iraqis when we’ve got Daesh to kill out in the west,” Lt. Gen. Paul Funk told The Associated Press, using another acronym for IS, which still controls territory straddling Iraq’s western border with Syria.

Clashes broke out earlier this month when federal forces retook the disputed city of Kirkuk and other areas outside the autonomous Kurdish region that the Kurds had seized when IS swept across the country in 2014. Most of the Kurdish forces withdrew without a fight, but tensions remain.

On Thursday, Prime Minister Haider al-Abadi rejected a Kurdish offer to “freeze” the results of the referendum, in which 90 percent voted to redraw the map. Iraq’s government has demanded the annulment of the vote and the transfer of border control and other infrastructure to federal forces.

The dispute has laid bare longstanding rifts in the coalition assembled to fight the Islamic State group that could complicate efforts to flush the extremists out of their last strongholds, or create an opening for them to re-emerge.

Funk said he would have preferred to spend recent weeks focused entirely on preparations for an operation launched Thursday to drive IS from its last pockets in the western Anbar province. But in addition to supervising that operation, he has been shuttling between the commanders of Iraq’s various security forces acting as a mediator in the dispute with the Kurds.

The troop movements and low-level skirmishes are also stretching the U.S.-led coalition’s intelligence and surveillance resources. Drones previously used to monitor the fight against IS have been diverted to watch flashpoints in the disputed territories, and the scattered clashes have impeded the movement of coalition vehicles and equipment.

Both the U.S.-led coalition and Iran rushed weapons and trainers to Iraqi and Kurdish forces in 2014 in order to stop the IS advance and begin to roll it back. But the various forces involved, including state-sanctioned mostly Shiite militias backed by Tehran, were never brought under a unified command.

Instead of trying to integrate Kurdish forces, known as the peshmerga, into Iraq’s military, coalition commanders divided up the battlefield during the various campaigns against IS. Iraqi and Kurdish forces, as well as the state-backed militias, known as the Popular Mobilization Forces, maintained separate command and control structures in their areas of responsibility.

“There should have been an equal focus on the military goal of defeating ISIS and keeping Iraq’s military institutions under a unified chain of command,” said Maria Fantappie, a senior Iraq analyst at the International Crisis Group.

“But there was less regard (from the international community) for how this process of arming different factions in Iraq could also undermine the political stability in the aftermath of ISIS.”

She acknowledges that, at least in the summer of 2014, when Iraq’s military had largely collapsed, the coalition likely had no option but to arm the various forces. “I’m not sure what alternative choice there could have been, frankly,” she said.

Funk, who assumed command of the U.S.-led coalition earlier this year, dismissed the idea that its military assistance laid the groundwork for future conflicts in Iraq, saying it had merely “enhanced” the abilities of existing forces. He added that modernizing a military is a generational endeavor, impossible to complete in just three years.

He said the eventual defeat of the IS group is “certain,” but that “policy issues” like stabilization and reconciliation will remain.

A State Department official said military cooperation against IS had strengthened “bilateral political ties between Baghdad and Irbil,” the Kurdish regional capital.

“Iraq is a complicated place. Its problems will not be solved overnight and often events take place that involve competing interests with no simple solutions,” the official added, speaking on condition of anonymity in line with regulations.

Fantappie, however, fears the further fragmentation of the country’s security forces once they no longer confront the shared threat of the extremist group. She said a new rift could open up between Iraq’s military and the Popular Mobilization Forces.

“In this case, against the Kurds, their interests converge, but in the future they may not,” she said.

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SUSANNAH GEORGE
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