The 108kg of drugs were discovered in the rudder area of the vessel, which had sailed from Colombia to Scotland.
The National Crime Agency arrested three Dutch men at Seamill Hydro Hotel in Ayrshire in connection with the find.
They also seized diving equipment, a rigid inflatable boat and an underwater scooter at the hotel.
The ship, named Cape Maria, was moored 2.8 miles north-west of Largs, Ayrshire, waiting for a berth at Hunterston terminal when authorities swooped on Friday.
Officers from Border Force and Police Scotland retrieved the drugs from the ship.
The captain and crew are not believed to have been involved at all.
The three Dutch men appeared at Leeds Magistrates' Court on Tuesday in connection with the incident.
They were remanded in custody.
Dutch authorities were also involved in the operation.