Serangan berlaku di wilayah Narino di barat negara itu, berhampiran sempadan Ecuador.
The academy was a military installation where cadets received training to become intelligence operatives and conduct military operations.
A prior round of peace talks had been suspended after an increase in violence on police stations.
The election is set to be the calmest in half a century of conflict in Colombia, with the former rebel movement FARC spurning jungle warfare for politics, and the ELN observing a ceasefire.
The ELN recently launched attacks that killed many police and military personnel.
The majority of the violence has occurred in Antioquia Department.
The ELN has claimed responsibility for the attacks.
The incident in Antioquia Department was part of a dispute between the ELN rebel group and the Gulf Clan drug gang.
United Nations Secretary-General António Guterres said that Colombia's ELN must take the initiative in normalizing the tumultuous situation in the country.