On Thursday afternoon, Mayor Willy Rodriguez of San José del Guaviare said that a large number of bodies had been discovered in the area.
"The bodies are lying in a pile; they need to be taken care of," the mayor told the AFP news agency.
The rival groups are fighting for control of territory and for power over drug trafficking and the many illegal mines found in the area.
Unrest has escalated in Colombia, where a presidential election is scheduled for May 31.
The FARC guerrillas and Bogotá reached an agreement in 2016, which led to breakaway groups.
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