"The Iraqi air force carried out a heroic operation targeting the convoy of the criminal terrorist Abu Bakr al-Baghdadi," Iraq's security forces said in a joint statement.
"His health status is unknown," it said, adding that the leader of the IS jihadist group was "transported in a vehicle" after the strike.
Iraqi security sources have previously said Baghdadi had been injured or killed in past strikes, but such claims were either never verified or later denied.
Iraqi aircraft struck Baghdadi's convoy as it was "moving towards Karabla to attend a meeting of the Daesh terrorist leaders", the statement said.
"The meeting place was also bombed and many of those leaders were killed and wounded," it said, adding that it would later release names.
Daesh is an Arabic acronym for IS, which last year proclaimed a "caliphate" straddling Iraq and Syria.
Karabla is located on the Euphrates river barely five kilometres (three miles) from the border with Syria.
It said the operation was conducted in coordination with Iraq's interior ministry intelligence services and the joint operation command centre that includes military advisers from the US-led coalition.
The health and whereabouts of Baghdadi, who has a USD 10 million US bounty on his head, are the subject of constant speculation.
He was reported wounded multiple times over the past year and his apparent survival has only added to mystery surrounding the IS chief.
According to an official Iraqi government document, Baghdadi was born in Samarra in 1971 and has four children with his first wife - two boys and two girls born between 2000 and 2008.
Baghdadi apparently joined the insurgency that erupted after the 2003 US-led invasion of Iraq, at one point spending time in an American military prison in the country's south.
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