The decision to remove the governor, Najmaddin Kareem, came after Kirkuk - an oil-rich province claimed by both the central government in Baghdad and the autonomous Kurdish region in northern Iraq - chose to take part in the KRG referendum.
Earlier in the day, the parliament received a demand from Prime Minister Haider al-Abadi asking the lawmakers to vote to remove Najm al-Din Kareem from his post as governor of Kirkuk province, the state-run Iraqiya Channel said.
Turkey and the US are also opposed to the vote, with Ankara saying regional stability depended on Iraq's unity and territorial integrity.
Turkey, too, rejects the planned referendum, saying the region's stability depends on the unity of Iraq and the maintenance of its territorial integrity.
Meanwhile, the leader of the Kurdish region of Iraq, Massoud Barzani, said the referendum is "a natural right".More news: Your letters: Suu Kyi, Dalai Lama must halt Rohingya massacre
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Jaafari was in Cairo for an Arab League summit where the closing statement included a resolution calling a Kurdish independence referendum this month unconstitutional, mirroring the stance of Iraq's central government and national parliament. In a statement similar to Ankara's words, Baghdad said Iraqi Kurdish leaders must be prepared to "face the consequences" if they unilaterally declare independence.
He said he has the full backing of his Patriotic Union of Kurdistan, his party's office in the province, and all Kurdish parties.
Karim said he will keep his post, adding he has received phone calls from Kurdish officials such as President Barzani who offered their support.
Jaafari said the worldwide community must offer financial and other support to Iraq for the rebuilding of Mosul and other cities retaken from Islamic State. But the statement said Israel "supports the legitimate efforts of the Kurdish people to attain a state of its own".
Widely seen as the world's largest stateless people, most Kurds are spread between Iran, Iraq, Syria and Turkey. He explained that the law for the Iraqi provincial election passed in 2008 stipulated that Kirkuk, unlike the rest of the Iraqi provinces, would not come under the authority of the office of the Iraqi Prime Minister.