"Operations are still continuing" in the Arauca department along the Venezuelan border, Velasquez told reporters, saying the dead included four men and two women.
Founded in 1964, the ELN had more than 5,800 combatants in 2022, according to authorities. It is Colombia's last active guerrilla group.
On June 9, Colombian negotiators signed a six-month ceasefire agreement with the ELN, which is set to begin on August 3.
Both Colombian President Gustavo Petro and ELN leader Antonio Garcia attended the signing ceremony in Havana, Cuba.
If it holds, the ceasefire would be the longest ever agreed to by the ELN, which has taken part in failed negotiations with Colombia's last five governments.
Garcia on Tuesday voiced skepticism that the government would abide by the agreement, saying on Twitter that Colombian special forces had recently been deployed in regions where the guerrillas have operated for decades, such as in Arauca.
"It is known that they will not comply with orders to stop military and intelligence actions... They are already located in specific territories and ready to act militarily against the ELN," Garcia said without mentioning the six deaths.
Petro, himself a former guerrilla, came into power last August pledging a policy of "total peace."
His government's negotiations with the ELN come after the historic 2016 deal that saw the Revolutionary Armed Forces of Colombia (FARC) rebel group lay down their arms.
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