It sank as police tried to intercept it in the Aldan inlet in the Galicia region at the weekend. It’s believed the crew tried to sink it on purpose.
Two Ecuadorian nationals have been arrested but another person managed to escape.
Authorities could not confirm the origin of the sub or the intended recipient, but media reports said police suspect it is from Colombia.
The 20-metre (65ft) sub was towed into port at Aldan – in the northeast of the country – and refloated with the help of divers and balloons.
Police divers pulled out one package of cocaine on Monday but there are believed to be tonnes on board.
Spanish authorities said it was the first time they have found a submarine being used to smuggle drugs into the country.
They had been monitoring its movements in recent days in collaboration with international police.
In September, a sub with five tonnes of cocaine worth about £133m was captured by the Florida coastguard in the eastern Pacific.
