Iraq's autonomous Kurdish area Friday accused Prime Minister Haider al-Abadi of "hatred" of the Kurds after he compared their September independence referendum to acts by the Islamic State group.

At a meeting of his Dawa party on Wednesday, Abadi said: "To have maintained Iraqi unity and prevented the crime of partition is a victory as great as that against Daesh (IS)."

After a September 25 independence referendum held in defiance of Baghdad, federal security forces seized control of disputed zones in the north that had been held by the Kurds.

"Some people wanted to use the war against Daesh to divide the country and facilitate a separation, but thank God, the Iraqis through their conscience, the Kurds and Arabs as well as the peshmerga (Kurdish fighters) who fought Daesh refused to turn their guns on the Iraqi army and federal forces," Abadi said.

"They refused to obey orders... to fight the Iraqi forces and patriotically obeyed their consciences," he said.

On Friday, the Kurdish autonomous region's peshmerga ministry said in a statement that it "regretted" Abadi's comments.

"His declaration demonstrates the depth of his thinking and his hatred for the people of Kurdistan.

"But history has proven that no one or any force can break the will of the Kurdish people," it added.

September's referendum returned a resounding "yes" vote for Kurdish independence.

On November 20, Iraq's supreme court declared the vote to be unconstitutional, in a decision hailed by Abadi who said his government "rejected this referendum and refused to have anything to do with it".