Iraqi security forces and Popular Mobilization Forces patrol in Tuz Khormato, that was evacuated by Kurdish security forces, 130 miles north of Baghdad, Iraq, on Monday. Two weeks after fighting together against the Islamic State, Iraqi forces pushed their Kurdish allies out of the disputed city of Kirkuk, seizing oil fields.

KIRKUK, Iraq — Two weeks after fighting together against the Islamic State, Iraqi forces pushed their Kurdish allies out of the disputed city of Kirkuk on Monday, seizing oil fields and other facilities amid soaring tensions over last month’s Kurdish vote for independence.

The move by the Iraqi military and its allied militias so soon after neutralizing the Islamic State in northern Iraq hinted at a country that could once again turn on itself after disposing of a common enemy.

Civilians and federal troops pulled down Kurdish flags around the city. Kurdish Gov. Najmaddin Karim, who had stayed at his post despite being dismissed by Baghdad weeks ago, fled to Irbil, the capital of Iraq’s autonomous Kurdish zone.

Revelers waving Iraq’s national flag and the flag of its Turkmen minority flooded central Kirkuk in an evening celebration. But it was the Shiite sectarian chants heard above the din of the rally that underscored the coming political battles between Iraq and its Kurdish region.

Iraqi forces were supported — as they always are now in major operations — by the country’s Popular Mobilization Forces, a predominantly Shiite militia coalition that the Kurds see as an instrument of Iranian policy.

In their bid to keep Kirkuk and its oil-rich countryside, Kurdish leaders whipped up fears that the central government in Baghdad is dominated by Tehran and would oppress Kurds if they recaptured the ethnically mixed city.

Their fears were further affirmed after Iran came out forcefully against the Kurdish region’s nonbinding referendum for independence on Sept. 25 and then closed its official crossings to the region on Sunday.

Iraq’s Kurds, too, remember the brutal campaigns waged by Saddam Hussein, himself an enemy of Tehran, against the minority, including a poison gas attack on the town of Halabja in 1988 that killed thousands.

As Arab and Turkmen revelers celebrated the change of power in Kirkuk, thousands of Kurdish residents, fearful of federal and militia rule, packed the roads north to Irbil.

But Baghdad was eyeing its Kurdish partners warily as well. Prime Minister Haidar al-Abadi said he was reclaiming a city that was never within the legal boundaries of the Kurdish autonomous region.

When Iraq’s armed forces crumbled in the face of an advance by Islamic State group in 2014, Kurdish forces moved into Kirkuk to secure the city and its surrounding oil wells. The city is 32 kilometers (20 miles) outside the Kurds’ autonomous region in northeast Iraq.

Baghdad insisted the city and its province be returned, but matters came to a head when the Kurdish authorities expanded their referendum to include Kirkuk. To the Iraqi central government, that looked like a provocation.