The photograph, the first of its kind published by an official source, provides a rare glimpse of the man leading a militant group blamed for killing countless Iraqis, as well as fighting the regime of Syrian President Bashar al-Assad.
The black-and-white picture shows a balding man with a beard wearing a suit and tie.
"Intelligence forces have obtained a recent portrait of Abu Bakr al-Baghdadi, and they also got three handwritten letters," said the statement accompanying the photograph, published on the ministry's website.
Baghdadi's group has been blamed for a litany of attacks across Iraq in recent months, and ISIL has been involved in a deadly standoff with government forces in western Iraq's Anbar province.
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In Syria, ISIL has also been fighting not only forces loyal to Assad but also fellow rebel groups. The ISIL leader has, however, reached out to other rebel groups in a bid to curb the infighting.
ISIL, which was previously the Islamic State of Iraq, was formed in April 2013 when Baghdadi sought to merge his group with Al-Nusra Front, but they rejected the alliance and pledged allegiance directly to Al-Qaeda chief Ayman al-Zawahiri.