It was not clear in the statement sent by the Joint Operations Command coordinating the fight against the jihadists in Iraq whether the world's most wanted terrorist had been hit.
An intelligence cell monitored a convoy that the statement said transported Baghdadi from the area of Raqa, the jihadists' main Syrian stronghold, across the border to the Al-Qaim area in western Iraq.
The statement said Iraqi air force F-16 jets struck a meeting of top IS commanders on February 11, but did not make clear whether Baghdadi was present.
The Iraq-born Baghdadi, who proclaimed a "caliphate" straddling Iraq and Syria in June 2014, was not one of those names.
Iraq's military said dozens of other IS militants were also killed in other strikes in the same area as part of the operation.