Boubaker el-Hakim was reported by American defence officials to have been killed in November, in a US drone strike in Raqqa, ISIS's de facto capital in Syria.
Iraqi intelligence supplied information to the Syrian airforce to carry out a series of strikes on ISIS headquarters and hideouts in Syria, including one believed to belong to el-Hakim, an Iraqi military statement said.
Aircraft from Syrian President Bashar al-Assad's airforce targeted several locations in Raqqa and Albu Kamal, near the Iraqi border, said the statement, without indicating the location of el-Hakim's headquarters or the date of the raids.
An Iraqi military spokesman told Reuters el-Hakim's headquarters were destroyed but it wasn't clear if he was killed.
In 2015 Iraq and Syria established a joint committee with Russia and Iran, Assad's main foreign backers, to share intelligence about ISIS.
El-Hakim was believed to have been involved in planning the January 2015 attack on Charlie Hebdo, a weekly known for its satirical covers ridiculing political and religious leaders.
ISIS declared a 'caliphate' spanning parts of Iraq and Syria after it captured the Iraqi city of Mosul in mid-2014.
The hardline group has since lost most cities it captured in Iraq and its terrorists are now surrounded in parts of Mosul by US-backed Iraqi government forces.
A US-backed offensive is also under way to capture Raqqa, involving a Syrian Kurdish-Arab alliance.
(Reporting by Maher Chmaytelli, Editing by Andrew Bolton)