With Iraqi troops making steady progress in their assault to retake Mosul from the jihadists, a US defence official said Baghdadi had fled to avoid being trapped inside.
It was the latest sign that IS is feeling the pressure from twin US-backed offensives that have seen it lose much of the territory it once controlled in Iraq and Syria.
Speaking to reporters in Washington, the defence official said Baghdadi had left Mosul before Iraqi forces seized control of a key road at the beginning of this month, isolating the jihadists in the city.
"He probably gave broad strategic guidance and has left it to battlefield commanders."
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Baghdadi, who declared IS's cross-border "caliphate" at a Mosul mosque in 2014, in an audio message in November urged supporters to make a stand in the city rather than "retreating in shame".
Iraq launched the offensive to retake Mosul -- which involves tens of thousands of soldiers, police and allied militia fighters -- in October.
After recapturing its eastern side, the forces set their sights on the city's smaller but more densely populated west.
The military said yesterday they had also taken the infamous Badush prison northwest of Mosul where IS reportedly executed hundreds of people and held captured Yazidi women.
Today Iraqi forces were "combing the city centre area to defuse (bombs in) homes and shops and buildings," Lieutenant Colonel Abdulamir al-Mohammedawi of Iraq's elite Rapid Response Division told AFP.
Forces were also "searching for snipers in the city centre," Mohammedawi said.
"Currently there is no order from the operations command to advance toward the Old City. We will advance when this order is issued," Mohammedawi said.
Hundreds of thousands of civilians are believed to still be trapped under IS rule in Mosul.
Those who did manage to escape the city said the jihadists were growing increasingly desperate.