The remains of 240 victims have already been unearthed and half of them identified, according to Attorney General Mario Iguaran.
Some of the graves have been found along major roads, dug only 1 metre deep by those who "had no interest in hiding their crimes," Mr Iguaran told a press conference.
The family of 13 of those victims have been given their remains in a ceremony in San Onofre, nearly 600 kilometres north of the capital Bogota.
Remains of another 77 people, who authorities believe were killed between 1996 and 2003, have been discovered near San Onofre, but have not yet been identified.
"We are digging up the truth," said Mr Iguaran who announced the findings based on the testimony of witnesses and demobilised fighters.
The investigators rely on the testimony of civilian witnesses in the countryside, who have been emboldened by the country’s relative peace since a 2003 agreement. "Hopefully the country won't be afraid to face the truth," Mr Iguaran added.
Graves in AUC areas
Most of the graves have been discovered in areas once controlled by the United Self-Defence Forces of Colombia, or AUC.
Under a 2003 peace accord with the government, more than 30,000 AUC fighters have handed in their weapons, renounced violence and agreed to confess their worst crimes in exchange for a maximum of eight years in jail.
If the AUC leaders honour their agreement, human rights groups believe that the number of civilian victims killed and left in graves could exceed seven thousand.