Al-Maliki did not say why the governor was sacked, but the move came after Kirkuk's provincial council voted to take part in a referendum on Kurdish independence slated for later this month.
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.
Iraqi Kurdish leaders must be prepared to face the consequences if they unilaterally declare independence and find implementation more hard than they expected, Iraqi Foreign Minister Ibrahim al-Jaafari said on Wednesday.
Ankara has warned Iraq's autonomous Kurdistan Regional Government (KRG) that there will be a "price to pay" for its insistence on holding an independence referendum later this month, calling on the administration in Arbil to think again.
On Tuesday, the leader of Iraq's Kurds, Massoud Barzani, said he would press ahead with the 25 September referendum despite a vote by Iraq's parliament rejecting it. "If any authority around the world... concludes that (Iraq's Kurds) deserve or merit an independent entity of their own, we appreciate that position".
Baghdad has repeatedly criticized the move and the Iraqi Parliament has already voted against the referendum.
Turkish presidential spokesman Ibrahim Kalin urged the Iraqi Kurdish government to "return from this wrong decision as soon as possible".
The United States and other regional countries like Iran and Turkey are opposed to the referendum as that could destabalize Iraq.
Israel "supports the legitimate efforts of the Kurdish people to achieve their own state", Netantahu said in a statement.
Turkey - which for over three decades has battled the outlawed Kurdistan Workers' Party (PKK) in its southeast - is strictly opposed to any move to a Kurdish state anywhere in the region.
The EU also declared its support for the territorial integrity of Iraq while the USA and Kurdish opposition Goran Movement demanded the postponement of the referendum.