Two Ecuadorian men were arrested as part of the operation Sunday in the seaside town of Cangas near the border with Portugal, a spokesman for the central government's representative in Galicia said.
“A diver managed to enter the submarine on Monday and removed a bundle of cocaine from inside,” he told AFP.
Police were on Monday trying to refloat the vessel and they will not be able to determine the total amount of drugs on board until they have done so, he added.
But a source close to the investigation told AFP the submarine was “likely” transporting “several tonnes (of cocaine) but this is just an estimate”.
Spanish media said the vessel was carrying over three tonnes (6,600 pounds) of cocaine from Colombia.
Guardia Civil officers work to refloat the submarine. Photo: AFP
The submarine, about 20 metres (65 feet) long, came from South America, another source close to the investigation said without specifying which country the vessel departed from.
“It is not the first time but we don't see this every day” in Europe, the source added.
Drug traffickers, especially from Colombia, have been caught using submarines to transport cocaine into Mexico, and from there into the United States.
The gangs often pay unemployed engineers desperate for money to design and make the submarines, said Wilder Alejandro Sanchez, a defence and geopolitics analyst at a US-based think-tank, the Center for International Maritime Security (CIMSEC).
Most are only semisubmersible — a ship partially submerged that cannot fully dive like a submarine — but some are able to go 30 metres under water, he added.
“They are becoming more and more modern and complex,” he told AFP.
In September the US Coast Guard, with the aid of the Colombian navy, intercepted a submarine carrying over five tonnes of cocaine off the coast of South America.
Galicia, one of Spain's poorest regions, is a top entry point for cocaine into Europe. A maze of coves, caves and inlets dot its rugged coastline, making it a smuggler's paradise.
Spain accounted for the second-highest proportion of cocaine seizures in the European Union last year after Belgium, with 41 tonnes apprehended.