Specialist agents, including members of Britain's Serious Organized Crime Agency, conducted a dawn raid on March 15 while the ship was in the Atlantic Ocean, some 700 miles southwest of Portugal's Cape Verde islands.
"It is the largest operation so far in 2013 in our fight against drug trafficking," said Ignacio Cosido, Spain's director general of police.
Five crew aboard, four Brazilians and one Korean, were arrested and four alleged organizers—including the suspected Venezuelan mastermind—were rounded up the next day in the northern Portuguese city of Porto.
"He is a well-known person," Cosido said of the main suspect. "He has a background in drug trafficking and is an important member of that world."
Cocaine bales hidden in a bow locker and a backpack with a large amount in U.S. dollars were seized. The cocaine arrived at the naval dockyard of the Canary Island port of Las Palmas de Gran Canaria on Saturday, Cosido said.
The gang included a large group of Venezuela-based cocaine suppliers, the ministry statement said.
Earlier Saturday Spanish authorities said they had also seized 590 kilograms (1,300 pounds) of cocaine discovered inside a sailboat moored at a private dock and arrested two Eastern European men aboard.
The suspects were identified only as a 60-year-old Bulgarian and a 30-year-old from Serbia, one of whom was armed with a loaded 9mm pistol.
The operation began when a suspicious vessel sailing in international waters was found heading toward Spain's Mediterranean coast.
Agents observed the yacht entering the Sotogrande marina in southwestern Spain without lights and tying up at a private jetty. Investigators acting under instruction from a court in San Roque also searched several houses in that city and in Marbella.
The judicial authority ordered the suspects' imprisonment. The arrest took place last week but an exact date was not given.