Interior Ministry spokesman Saad Maan told The Associated Press that the assailants ambushed a car last night carrying the clerics in the mostly Sunni district of Bab al-Zubeir near Basra, shooting dead the three and seriously wounding two other clerics travelling with them.
The ministry, he said, was investigating the killings. He gave no other details.
There was no claim of responsibility for the ambush and no reports of retaliatory attacks by Sunnis.
Shiites make up a majority of Iraq's estimated 30 million people and have dominated successive governments since the 2003 ouster of Saddam Hussein, a member of the Sunni minority who oppressed the Shiites during his rule.
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The attack followed a visit to Basra this week by Shiite Prime Minister Haider al-Abadi and his tour of a Sunni area north of Baghdad on New Year's Eve. Al-Abadi on both visits spoke emphatically about the need for all of Iraq's religious and ethnic communities to close ranks in the face of the threat posed by the Islamic State group.
Speaking later on state Iraqi television, the association's head, Khaled al-Mullah, said the Islamic State group and its supporters were the only beneficiaries of the attack.
In other violence today, a roadside bomb exploded in central Baghdad, killing four civilians and wounding 12, police and hospital officials said. They spoke on condition of anonymity because they were not authorised to speak to journalists.