Police were only able to determine the amount of drugs inside after they managed to refloat the vessel three days later and tow it to a nearby port.
They found 152 bundles with three tonnes of cocaine, Spanish police said in a statement.
Drug traffickers, especially from Colombia, have been caught using submarines to transport cocaine into Mexico, and from there into the United States.
Police said: "This is the first time that this system of transporting drugs has been detected in Europe."
The drugs had a street value of 100 million euros, the central government's representative in Galicia, Javier Losada de Azpiazu, told reporters.
"This is a historic operation, which will mark a before and after," he said.
A source close to the investigation had previously told AFP that the submarine came from South America but Losada de Azpiazu said police were still working to determine its exact origin.
A total of 240 agents took part in the operation, which was carried out in conjunction with police from Brazil, Portugal and the United States.
Two Ecuadorian nationals were detained as they tried to escape from the submarine when police moved in. A third person is still on the run.
(With AFP)
