The army said five soldiers were injured in the attack, adding that it launched the assault on FARC-controlled territory in San Antonio de Getucha, in Caqueta province.
"We launched an operation deep in (FARC's) southern block with a goal of protecting our civilian population," the army said in a statement.
It added that intelligence sources indicated the FARC suffered an "undetermined number of dead and injured" in the fighting.
Earlier this week, the government and the leftist rebels had reported progress on the key issue of land redistribution in their peace talks to end Latin America's oldest insurgency.
But the reported progress comes amid renewed battles between the two sides, after rebels ended a self-imposed moratorium on fighting last month.
Since the Marxist guerrillas lifted their unilateral ceasefire on January 20, they have increased attacks on civilian and military targets, taken hostages and blown up oil and energy infrastructure in a bid to force the government to suspend hostilities.
On Tuesday, suspected FARC guerrillas killed a policeman and a boy and wounded 27 other people, many of them children, in a grenade and gunfire attack in the southern province of Guaviare.
