Ninety-seven kilograms of cocaine with a market value of €11 million have been intercepted by the police and customs in a joint operation.
The police said the drug was hidden on a cargo ship that entered the Freeport.
Divers of a security company commissioned by the ship's agents carried out an inspection on Sunday morning and saw a number of suspicious packages wrapped in plastic in a compartment at the bottom of the ship.
They immediately informed the authorities and the packages were then taken out of the compartment and onto land.
The Portugal-registered ship had left Colon in Panama on July 24 and was headed to Gioia Tauro in Italy. It entered the Freeport on Saturday evening.
The police said it did not seem the drug was intended for the local market.
An inquiry is being held.