The 49-foot craft was found Friday, 330 miles off the coast near the national park of Isla del Coco, Security Minister Fernando Berrocal said. Four people were arrested.
He said it was the first time such a vessel was seized near the coast.
Two Colombians, a Guatemalan and a Sri Lankan were arrested and taken to the U.S., where they will confront drug trafficking charges, while the submarine was taken to a Costa Rican Coast Guard station, he said.
So far this year, Costa Rican authorities have seized 18 tons of cocaine