Iraq’s Supreme Justice Council ordered the arrest of Kurdistan Regional Government Vice President Kosrat Rasul for allegedly saying Iraqi troops were “occupying forces” in Kirkuk.
A Supreme Judicial Council spokesman said the court considered Kosrat Rasul's remarks as an incitement to violence.
He made them in a statement condemning the withdrawal of Peshmerga fighters from Kirkuk and other disputed areas.
Baghdad launched an operation to retake them on Monday, three weeks after the Kurds held an independence referendum.
On Tuesday night, after the military operation concluded, Iraqi Prime Minister Haider Al-Abadi said the referendum was "a thing of the past" and offered "dialogue under the constitution".
KRG Peshmerga forces deployed into Kirkuk in 2014 when Iraqi government forces fell apart in the face of an offensive by ISIS insurgents, preventing the oilfields from falling into jihadist hands.
Rasul issued a statement on Wednesday lashing out on his own Patriotic Union of Kurdistan party amid reports that other leaders had ordered Peshmerga under their control not to resist the Iraqi troops as they advanced into Kirkuk.
There was only one serious clash on the outskirts of the city on Monday, which is reported to have left between three and 11 combatants dead.
Rasul said the territorial losses represented a "new Anfal for Kurdistan" - a reference to the campaign of genocide against Iraqi Kurds by Saddam Hussein's regime in 1987 and 1988.
On Thursday, a spokesman for the Supreme Judicial Council said a court in Baghdad issued an arrest warrant for Rasul in connection with the statement.
"The court considers these comments as provocation against the armed forces, under Article 226 of the penal code," the spokesman added.
The offense can carry a jail term of up to seven years or a fine.
Meanwhile, KRG Foreign Minister Fala Mustafa Bakir told broadcaster CNN that his side never meant to engage in war with the Iraqi army. He said there was a need for dialogue between the KRG and Iraq to enable a common understanding. The dispute, he added, was not about oil or the national flag but the future of two nations.
Crude oil flows through the KRG pipeline to the Turkish port of Ceyhan have been disrupted by a gap between incoming and outgoing personnel since Baghdad’s retaking of Kirkuk.
An Iraqi oil ministry official in Baghdad said on Thursday that Iraq would not be able to restore Kirkuk’s oil output to levels before Sunday because of missing equipment at two fields.
The official accused the Kurdish authorities previously in control of Kirkuk of removing equipment at the Bai Hasan and Avana oil fields, northwest of the city.