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The 20-metre semi-submersible vessel was intercepted off the coast of Galicia in the north-west of the country on Sunday and 3,000kg of cocaine, divided into 152 packages, was found on board.
The drugs - which are reported to be worth around €100m (£85m) - were subsequently removed from the craft after it was floated and brought into the port of Aldán in the Galician province of Pontevedra.
Two Ecuadarian members of the crew were arrested after allegedly deliberately sinking the vessel as police closed in before attempting to swim to shore, while a third member of the crew is yet to be found by authorities.
The seizure of the vessel was the result of a joint operation between police forces from Spain, Portugal, the US, the UK and Brazil and was initiated after the EU's Maritime Analysis and Operation Centre informed Spain's Counter-Terrorism and Organised Crime Intelligence Centre that a suspicious vessel was headed in their direction, from across the Atlantic Ocean.
Authorities intercepted the boat after tracking its progress for 10 days.
In a statement, the Guardia Civil said that while the use of so-called 'narco-submarines' is common practice in the Americas, it is believed to be the first time such a vessel has been caught in European waters.
The statement read: "Conditions at sea meant that the semi-submersible wasn't able to deliver the drugs to a second vessel.
"Its crew members then headed towards the coast, where they scuttled and abandoned the vessel. The manoeuvre was detected by a Guardia Civil patrol using night-vision goggles, who then noted the boat's arrival point and the subsequent fleeing of its crew.
"Although the use of these submarines is very common in the Americas, this is the first time that such a transportation system has been used [here].
"The investigation into both the origin of the drugs and the gang that was set to handle them in Spain is ongoing."
An agent from the Spanish drug unit told ABC they had long been on the lookout for narco-submarines.
They said: "We had been hearing about this type of transport for years, the Americans had told us about it and some drug dealers who were detained in operations before 2010, who later turned away, but we had never seen them."
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