Over four tonnes of the drug were being transported from Montevideo, Uruguay, to Antwerp, Belgium, when they were intercepted by authorities during a routine check two weeks ago.
The shipment, listed as soya beans, was hidden in over 200 black sports bags inside a shipping container.
The drugs have since been destroyed under strict security, officials said.
“Assuming that this likely high-purity cocaine can be cut to triple the amount for street sale, the 4.5 tonnes has a street value of approximately €1 billion”, the Hamburg Customs agency said in a statement.
It added that the Hamburg prosecutor’s office were now investigating the intended destination of the container.
German officials say the discovery reflects their growing ability to interrupt international drug smuggling. But they also warn that the size of the haul indicates that South American drugs cartels are growing bolder.
Hamburg is Europe’s third biggest port, and the largest in Germany.