President Ivan Duque said he had authorized the military operation in rural areas of Colombia's south.
In a statement welcoming the raid, Duque dismissed the group as "a gang of narco-terrorist criminals who are residuals of what was known as the FARC, and who are part of the criminal structures that seek to challenge Colombia."
Friday's operation was "a clear message" to the group to lay down their weapons, he said.
Defense Minister Guillermo Botero, who said the operation had taken place in the San Vicente del Caguan region, wrote on Twitter: "The criminals are warned: they surrender or they will be defeated."
On Thursday, Duque said he would send a special army unit "with reinforced intelligence, investigation and mobility capabilities" to hunt down dissident leader Ivan Marquez and other holdouts.
That same day, Marquez announced a return to arms in a video message, accusing Duque's government of betraying the accord, under which most of the FARC's 7,000 fighters disarmed after half a century of conflict.
The whereabouts of Marquez, the Marxist FARC's number two leader and chief negotiator of the 2016 peace agreement, have been unknown for more than a year.
Marquez and a fugitive rebel colleague, Jesus Santrich, have distanced themselves from the peace deal.
Santrich, who went underground earlier this year after the United States sought to have him extradited on drug charges, also appeared in the video.
Marquez said his forces would coordinate with Colombia's last active rebel group, the National Liberation Army (ELN), "and those comrades who have not folded up their flags."
The United States, a key ally of Duque's conservative government, denounced Marquez and his allies.
"We strongly repudiate recent calls by some individuals to abandon the FARC's commitments under the 2016 peace accord," Secretary of State Mike Pompeo said in a statement.
"We stand resolutely with the government of Colombia, President Duque and the Colombian people in their efforts to ensure justice and the lasting peace and security that the people deserve."
Although most of the FARC fighters laid down weapons to return to civilian life, around 2,300 have refused to do so.
"Colombians must be clear that we are not facing a new guerrilla, but facing the criminal threats of a gang of narco-terrorists who have the shelter and support of the dictatorship of Nicolas Maduro," Duque said.
Duque, on a visit to Sincelejo in northern Colombia, said in Friday's statement on the raid that the FARC unit's leader, who went by the name Gildardo Cucho, was among those killed.
He described Cucho as "a criminal dedicated to drug-trafficking, kidnapping, intimidation of social leaders and who intended to be part of that threatening structure that yesterday was presented to the country as a new guerrilla, which it is not." – Rappler.com