Police arrested 16 people and seized the yacht as well as a catamaran, several vehicles, a gun and cash in the probe, the ministry said in a statement.
Spanish authorities intercepted the yacht on September 2nd in international waters north of Portugal's Azores islands and arrested its four crew members — two Estonians, a Serbian and a Spaniard — after finding more than 800 kilos of cocaine on board.
Police arrested another 12 people in the southern Spanish region of Andalusia suspected of involvement in trafficking of the narcotics.
"With this operation, a network of drug-traffickers who offered their services to South American drug suppliers has been dismantled," the statement said.
The police did not say how much the drugs were worth.
In July, Spanish authorities seized 500 kilos of cocaine from a yacht off the Canary Islands in the Atlantic, breaking up a ring that smuggled drugs from Latin America to the Spanish archipelago.
Spain is a key entry point for drugs bound for Europe.
Spanish authorities seized 20.7 tonnes of cocaine last year, 24.9 percent more than in the previous year, and 325.5 tonnes of hashish, down 8.5 percent from 2011, according to the interior ministry.
That represented 41.2 percent of the total amount of cocaine seized in Europe last year and 74 percent of the hashish.