The cocaine was stored in 1-kilogram packets hidden inside the 40-foot container, which was en route from Ecuador to Slovenia, DPA reported.
It was discovered after a scan at Malta's Freeport noted flagged discrepancies in the weight of boxes containing the drug and others inside the container.
Customs officials estimated the drug's value at anything between 90 million and 100 million euros.
The haul is the largest ever drugs bust in Maltese history, breaking a 612-kilogram cocaine seizure record made late in 2020.
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