The fate of the IS leader was unknown, it said. The strike has not been independently confirmed.
The attack is said to have happened in western Anbar province, near the Syrian border.
There have previously been reports that the IS leader has been killed or seriously injured in attacks, but none was subsequently confirmed.
The Iraqi air force "bombed the convoy of the terrorist Abu Bakr al-Baghdadi while he was heading to Karabla to attend a meeting" with Daesh (IS) commanders", Sunday's statement from an interior ministry intelligence unit said.
Baghdadi was "transported in a vehicle" after the air strike but "his health status is unknown," the statement said.
"The location of the meeting was also bombed and many of the group's leaders were killed and wounded."
Interior ministry spokesman Saad Maan told AFP the strike happened at midday on Saturday.
There has been no official IS response; however one IS media representative said the government's claim aimed to boost the morale of its troops.