The unmanned submersibles are apparently capable of carrying up to 200kg (441lbs) of cargo.
As part of the 14-month investigation, eight people have been arrested in Cadiz, Malaga, and Barcelona.
Police say it means they have broken up a gang suspected of building the vehicles and supplying them to drug smugglers across Europe.
Spanish police say it is the first time they have discovered an underwater vehicle capable of being operated unmanned.
