Kurdish forces were withdrawing from Kirkuk on Monday as Iraqi federal forces moved in to the disputed city and seized oil fields and other infrastructure amid soaring tensions over last month's Kurdish vote for independence.
Kurdish forces, who were key allies in the US-backed offensive against IS, are refusing to surrender positions they took during the fightback against the jihadists over the past three years.
The JOC said its forces had retaken the K1 military base northwest of Kirkuk, the military airport east of the city and the North Oil Company and Baba Gargar oil fields, two of six in the disputed region.
Both Kurdish parties control their own Peshmerga units.
Last Friday, US President Donald Trump announced that the IRGC was the target of new American sanctions, describing Iran's leading military institution as the "corrupt personal terror force and militia" of the regime's supreme leader that has "hijacked" large portions of the economy "to fund war and terror overseas".
The US-led task force said it was aware of "a limited exchange of fire during predawn hours", which it believed was "a misunderstanding and not deliberate as two elements attempted to link up under limited visibility conditions".
A statement by the US-led worldwide military task force in Iraq described the clashes outside Kirkuk as a "misunderstanding". The Kurdish region is presently entitled to 17% of Iraq's federal budget, of which the Kurds are expected to try to negotiate a bigger share, in addition to greater autonomy.
The Kurdistan Workers' Party (PKK), which has fought a more-than-three-decade-long insurgency against Turkey, also has forces deployed in Kirkuk in support of the PUK.More news: Austria shifts to the right, empowering nationalists
Iraqi Army Captain Hamed al-Obeidi told Anadolu Agency that "hundreds" of Kurdish families had recently fled Kirkuk following the arrival of Iraqi government forces to the city's southern entrance.
The crisis is raising fears of fresh chaos in Iraq just as the country's forces are on the verge of routing the Islamic State group from the last territory it controls in the country. His claims could not be independently verified.
Popular Mobilisation is a mainly Shi'ite Iraqi paramilitary force trained and armed by Iran, which is providing support to the Iraqi operation in Kirkuk, according to state TV. Kurds consider it the heart of their homeland; they say it was cleansed of Kurds and settled with Arabs under Saddam to secure control of the oil that was the source of Iraq's wealth.
Pro-PUK forces were deployed south of the city, including at oil fields, while fighters loyal to the rival Kurdistan Democratic Party (KDP), linked to Iraqi Kurd leader Massud Barzani who initiated the referendum, were deployed to the north.
Tension has steadily mounted between Baghdad and the Erbil-based KRG since September 25, when Iraqis in KRG-controlled areas - and in several disputed territories, including Kirkuk - voted on whether or not to declare political independence.
State-run Iraqiya television said the military had also captured a refinery, a gas plant and a main road in Kirkuk, which has emerged as a flashpoint in the power struggle between the federal government in Baghdad and the Kurdistan Regional Government. Iraqi forces advanced into the contested province with the goal of returning to positions they held before 2014, when they fled in the face of an Islamic State push. "IS remains the true enemy of Iraq, and we urge all parties to remain focused on finishing the liberation of their country from this menace".
The presence of the Shiite militias, some of which are armed and funded by Iran, is a particularly sensitive issue for the Kurdish forces.
Iraqi Prime Minister Haider al-Abadi said the operation was necessary to "protect the unity of the country, which was in danger of partition" because of the referendum.