The rebel groups are fighting each other in the Guaviare region of the Amazon, where they seek to gain control over cultivation areas and drug smuggling routes, illegal mining and direct extortion of local populations.
Both groups originate from the feared guerrilla group FARC, which ended armed operations under a 2016 deal with Bogotá.
According to Colombia's military, the death toll could rise.
One group is led by Ivan Mordisco, who is also Colombia's most wanted person, and the other group is led by a person with the pseudonym Calarca - that group is reported to have held talks with the Colombian government about a peace settlement.
