The International Criminal Court is investigating Alvaro Uribe, during whose term as president most of the extrajudicial killings occurred, Colombia Reports said Friday.
Uribe held office from 2002-08, a period in which the ICC alleges the Colombian military killed thousands of civilians.
ICC prosecutors are looking into so-called "false positives" in which the deaths of peasants and the urban poor were characterized as left-wing FARC guerillas killed in combat.
Uribe has said such deaths were "isolated events," but the ICC said Colombian prosecutors have presented more than 3,000 cases to the court.
The former president is also being investigated for allegations that, while governor of Antioquia, he formed a paramilitary bloc.
The former director of the Colombian Security Agency, Jorge Noguera, is serving a 25-year prison sentence after being convicted of using paramilitary assassins to kill members of the opposition.