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.

"Clashes broke out with fighters from Saraya al-Salam," a group loyal to prominent Shiite 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", without naming a group.

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

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 at the end of last year.

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