The ministry said that one Croat was lightly injured and four buses were damaged in the incident which occurred in downtown Belgrade around 5 am on Sunday.
The windshield of one bus was damaged around 1 am near Paracin, on the road between Nis and Belgrade, when a stone is believed to have been thrown at it. No one was injured.
The Croatian convoy left Serbia at 7 am today.
The ministry said that the Croatian convoy's drive through Serbia to Sofia was provided with heavy police protection and that there were no incidents.
The ministry added that every security measure was taken for the convoy following Interpol's information that the Croatian convoy would pass through Serbia and that some soccer fans were aggressive and violent.