Last July, another fully submersible "narcosub" was seized just across the border by authorities in neighboring Ecuador.
Previous drug-carrying vessels found in Colombia were only semi-submersible, meaning part of the structure always remained above the surface.
But the sub discovered Sunday can operate completely underwater, Col. Manuel Hurtado, chief of staff of Colombia's Pacific Command, told The Associated Press. He estimated it could hold eight tons of drugs.
The sub in Colombia was found in a rural area of Cauca province on the Timgiqui River about 275 miles (440 kilometers) southwest of Bogota, the capital.
Hurtado said intelligence reports and tips from informants led troops to the vessel. He said the sub was empty when soldiers found it and no one was arrested.
The 99-foot-long (30-meter) fiberglass boat has room for a crew of six and is powered by two diesel engines and has an air-conditioned interior, Hurtado said. He said it can submerge up to nine feet (three meters) deep and is equipped with a 16½-foot (five meter) periscope.
"The engines were already fully installed and ready to go," Hurtado said.
The sub had "the capacity to sail totally underwater and the ability to travel to the coast of Mexico without surfacing," he added. He said such a trip would take eight to nine days.
Hurtado estimated the vessel had taken six to eight months to build and cost about $2 million.
He said Colombia has seized at least 32 semi-submersible vessels designed to smuggle drugs over the last decade, including a dozen last year.