Media reports put the number of dead between four and six and said about 39 people were wounded.
A security official told Aswat al-Iraq an explosives-laden car driven by a suicide bomber exploded near the main entrance to the ministry.
The New York Times reported the bomber tried to break through an entrance to the compound housing the ministry, the police academy, several jails and a hospital. When security officers fired on the vehicle, the bomber detonated the explosives.
"When the explosion happened it was so loud I couldn't hear anything. I felt like I was in a different world," Ahmed Abed, a taxi driver whose car was damaged by the explosion, told the Times.
On Thursday, explosions across Baghdad killed more than 60 people. Within a two-hour window, nine car bombs, six roadside bombs and a mortar round all went off in residential, commercial and government districts in Baghdad, police told CNN.
No one has claimed responsibility for the attacks Thursday or Monday.