"They used to feel safe ... now they are living in caves they use to hide away," Juan Manuel Santos, the defence minister, told reporters at the caves in La Macarena region in Meta province, located southeast of the capital Bogota.
Troops were led to the caves after a tip-off from a Farc deserter.
Reporters at the site were shown weapons, landmines, surgical equipment and explosives discovered in camps surrounding the caves.
The Farc once controlled many parts of Colombia in its fight for what it called a socialist state.
As Latin America's oldest insurgency, the Farc has funded its struggle with drug trafficking, kidnapping and extortion.
But the movement lost three of its senior commanders last year and has suffered a string of military setbacks.