Eduardo Fernandez said the fiberglass submarine was nearly complete when police found it near the Pacific Ocean, in Tumaco, 370 miles southwest of Bogota.
"The ingenuity of drug traffickers is amazing," Fernandez told The Associated Press.
He said the vessel would have been used to carry cocaine to speed boats offshore, which would then take the drugs to Central America or Mexico, for eventual delivery to the United States.
The discovery came after authorities were tipped off to pieces of fiberglass and other construction material being transported to where the submarine was being built.
Fernandez didn't provide details of its size. But Colombian authorities have caught drug traffickers using subs on a few occasions. They have been small, fiberglass vessels that travel just below the surface. But in 2000, police on a raid of a warehouse near Bogota were stunned to find a 100-foot-long steel submarine being built to transport up to 150 tons of cocaine.