Eight ELN guerrillas were killed in an operation in the eastern province of Arauca and at least five rebels from the FARC guerrilla group were killed in the central province of Meta, a defense ministry spokesman told AFP.
He said the toll could rise as troops continue sweeping the two areas.
The army said in a statement that the operation in Arauca, which also involved the air force, navy and national police, targeted an ELN camp that was "responsible for attacks on civilians, roads and oil infrastructure in recent days."
Defense Minister Juan Carlos Pinzon is expected to travel to the region, which borders Venezuela, later today.
The Colombian government and FARC have been holding talks in Cuba since November 2012 aimed at ending the 50-year-old conflict, but no ceasefire has been declared.
President Juan Manuel Santos won re-election last month after campaigning largely on his promise to bring the peace process to fruition. He begins his new four-year term on August 7.