Kirkuk Governor Najmaddin Kareem said he had no intention of following Baghdad's dismissal order, issued at the behest of Prime Minister Haider al-Abadi.
A parliamentary majority in Baghdad voted in opposition to the September 25 referendum planned by the Kurdish Regional Government (KRG) prompting Kurdish lawmakers to walk out of the session, which was attended by 204 of parliament's 328 members.
The decision to remove the governor, Najmaddin Kareem, comes after Kirkuk - an oil-rich province claimed by both the central government in Baghdad and the autonomous Kurdish region in northern Iraq - voted to take part in a referendum set for September 25 on Kurdish independence.
In remarks to Asharq Al-Awsat newspaper, Member of the Supreme Council for the Referendum Mohammed Saadeddin said: "We are waiting for the meeting to be held by the President with the political leadership in Kurdistan over the next few days, to discuss the current situation and the alternative plan presented by the worldwide coalition".
A top US diplomat is calling on Kurdish leaders in Iraq to halt its contentious independence referendum in favor of an alternative. "I will stay in office", he told Reuters. Otherwise, the referendum would be held "at all costs", he added.
McGurk did not provide details of the "alternative plan" but he said he presented it to KRG leaders.
All Kurdish legislators boycotted Thursday's session, while Arab parliamentarians voted in favour of Karim's deposition, he said.
Both groups are based in Iraq.
Ownership of Kirkuk has always been disputed between Iraq and the Kurdish authorities. USA -backed Iraqi forces recently crushed IS fighters in Tal Afar in a swift 11-day battle, and they now are preparing to attack IS's last major stronghold of Hawija in Kirkuk province. But it is only in Iraq where they have achieved a recognised autonomy.
US officials say peshmerga's cooperation with the Iraqi army played a critical role in removing IS from Iraq's second-largest city of Mosul.
As Turkey ramps up its warnings against an independent Kurdistan, pro-government newspapers reported Wednesday an alleged deal to settle 200,000 Kurdish Jews in the new state, Al Monitor reported.