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Special forces commander Sherif Ismail was heading back to Baghdad after preparing the ground for a trip planned for Wednesday by premier Haider al-Abadi to the conflict-ravaged Nineveh province when he was killed.

"Clashes broke out with fighters from Saraya al-Salam," a group loyal to prominent Shia cleric Moqtada Sadr, a security source said, after a verbal altercation spiralled out of control.

"The general was killed and three of his men were wounded," the source told AFP on condition of anonymity.

The prime minister's office confirmed the death of Ismail and blamed "shots from undisciplined fighters", but fell short of naming a specific group.

Abadi had "ordered the immediate opening of an investigation", a statement added.

The violence comes two months ahead of legislative elections in Iraq that Abadi is hoping will see him remain in charge after claiming victory against the Islamic State group.

In December, Abadi's government declared "the end of the war" against IS, announcing that government troops were in control of the long and porous Iraqi-Syrian border.

Experts and officials, however, believe that jihadists hiding out in the desert still have the ability to strike and even to seize areas of Iraq, especially near the Syrian border.

Analysts have warned that the group would increasingly turn to guerrilla-style attacks as it was pushed underground after losing territory.

Meanwhile, Abadi has said he will stand for re-election as the head of a new coalition, rather than running under the banner of his Shia Dawa party.

His new "Victory Alliance" coalition would be a "cross-sectarian" list aimed at overcoming divisions and battling inequalities in the country, the 65-year-old prime minister has said.

Commentators have previously mooted a potential alliance between Abadi and Sadr's parties at the vote.