The huge haul - worth tens of millions of pounds - was found hidden in the rudder shaft of the giant bulk carrier as it moored off Largs after a major operation led by the UK's National Crime Agency (NCA).
The agency's elite officers - backed by the UK Border Force and police from Scotland and the Netherlands - swooped on the ship on Friday as it waited to dock at Hunterston after arriving from Colombia.
They also arrested three men at the nearby Seamill Hydro Hotel near Ardrossan and seized diving equipment, a rigid inflatable boat and an underwater scooter.
The men, who have not been named but are Dutch, appeared at Leeds Magistrates Court on Tuesday charged in connection with the find.
Authorities were unable to make public comment on the case while prosecutors in England and Scotland decided where it should be heard.
It is understood the seizure, although made in Scotland, was largely the result of ongoing intelligence about Dutch and English crime organisations.
The cocaine seized, which was wrapped in plastic and tied to the rudder shaft way under the ship waterline, weighed a total of 108kg.
After being mixed with cutting agent benzocaine, it could be worth as much as £30 million on the UK market. However, it is not thought to have been destined for Scotland.
The bulk carrier concerned, the Marshall Islands-registered Cape Maria, is currently in Hunterston. Its captain and crew are thought to have been unaware that the drugs had been hidden in their ship.
The ship left Colombia's Caribbean port of Santa Marta carrying coal in mid-April and arrived in the Firth of Clyde on Friday.
It is not the first bulk carrier to arrive in Hunterston with more cargo than its crew expected. Three years ago the then UK Borders Agency found 10kg of cocaine stuck under the MV Bulk Australia as it delivered another load of Colombian coal in the Ayrshire port.
Drug smugglers have increasingly resorted to piggy-backing on commercial shipping, with frogmen using limpet magnets or adhesives to stick their illicit cargo on to hulls.
The NCA operates in Scotland from the base it shares with Police Scotland and other law enforcement agencies at the Gartcosh Crime Campus.
Its arrests and seizures in Ayrshire last week are understood to have been sanctioned by the Crown Office, which also has a large presence at the crime campus and works closely with UK counterparts.
England's Crown Prosecution Service had expected to prosecute the case because most of the criminality alleged - although not the seizures and three arrests - took place in its jurisdiction.
However, NCA was last night unable to provide full details of its operation, citing restrictions imposed by the Crown north of the Border, which suggests prosecutors have yet to decide whether to hear the case in a Scottish or English court.