Over the weekend, the EMC rebel group urged delegations not to attend the COP16 meeting after the guerrillas were targeted in a military offensive in the southwestern Cauca department, where they are active.
In fighting that followed the raid, at least 20 people were wounded in the village of El Plateado.
Defense Deputy Minister Daniela Gomez told El Tiempo newspaper that authorities have assessed "the possibility of reprisals by organized armed groups" and the "presence of the public forces has been strengthened to deal with this situation."
Cali, the nearest big city to the EMC-dominated territory, will host the COP16 conference from October 21 to November 1.
Some 12,000 delegates from around the world are expected to attend.
They would include more than 100 environment ministers and 14 heads of state, including Brazil's President Luiz Inacio Lula da Silva and Mexico's Claudia Sheinbaum, according to the government in Bogota.
Colombia's President Gustavo Petro insisted over the weekend that "the security of COP16 is guaranteed."
A dissident faction of the disbanded FARC guerilla group, the EMC had previously threatened the summit, saying in July the meeting "will fail even if they militarize the city with gringos (Americans)."
It later declared a truce.
But the weekend offensive unleashed a new wave of violence, with Petro authorizing the bombing of guerrillas in response to a rebel attack with drones.
Some 3,500 EMC members are estimated to be active, involved in the drug trade and illegal mining, and fighting both the military and other groups competing for trafficking routes and territory.
Some 11,000 Colombian police and soldiers as well as UN security personnel have been deployed around Cali.
Cali Mayor Alejandro Eder said US officers are already on the scene to provide their Colombian counterparts with technical assistance and "reinforce counterterrorism capabilities."
Petro has sought to resolve Colombia's armed conflict with the EMC and other groups through negotiations.
But Ivan Mordisco, the main EMC representative in the Cauca department, abandoned the talks in April.
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