The narcotics were said to have arrived in Ukraine as part of a shipment of fruit from Ecuador.
"Law enforcement officers have discovered a shipment of 'elite narcotics' bound for an EU country. In total, 46 blocks of cocaine with a combined weight of 54 kilograms [119 lbs] were hidden in the ventilation hatches of a container. The estimated value of the seized narcotics on the black market could be up to $12 million", the border service said in a statement.
A criminal case has been opened in connection with the discovery. Any conviction could lead to prison sentences of up to 12 years.
The border service noted that the total weight of cocaine seizures at ports in Odessa region this year has already topped 500 kilograms (1,102 lbs).
In September, law enforcement officers uncovered 112 kilograms of cocaine in a container that arrived from Ecuador at the Pivdennyi port, in Odessa region.