The firefight, which comes as the ELN is observing a three-month ceasefire with the government in Bogota, happened last week in a remote area of the country's southwest, the official, Carlos Negret, told reporters.
Negret said ELN guerrillas had gone to a municipality near the Ecuador border to disarm a local farmers' resistance group, made up of alleged FARC dissidents, when the fighting occurred "resulting in the killing of 13 citizens."
He said the confrontation "totally goes against" the ELN's ceasefire with the government.
The dead included a pregnant woman and a man with a mental disability, as well as dissident members of the FARC -- the rebel group that signed a November 2016 peace deal with the government.
Negret said the ELN had also abducted a member of the farmers' resistance group.
The army had previously reported that four people were killed in the clash between two armed groups in Magui Payan municipality, near the border with Ecuador.
The area sits near one of the prize drug trafficking routes in the region and is the area with the largest amount of land under coca cultivation in Colombia.
The ELN warned on Monday that the ceasefire deal, which is due to expire on January 9, was at risk even though the parties had managed to sustain it and deliver humanitarian aid to the regions of greatest conflict.
Amnesty International warned in a report last month that the government should do more to protect communities terrorized by armed groups and that, a year after the peace deal with the FARC, "armed conflict is still very much the reality for millions across the country."