The news was another blow to the costly Eurofighter programme - and raised concerns over the use of the planes.
According to Germany's defence ministry, the defect discovered was in the rear fuselage of the twin-engine multirole fighter.
As a result, Berlin has decided to cut the time its Eurofighters spend in the air each year in half, from 3,000 hours to 1,500 hours.
The news website Spiegel Online reported that, in the worst case scenario, the fault could result in the plane's hull becoming unstable. It said Britain's Royal Air Force first detected the defect and also decided to halve the annual flight hours so as not to overstress the jets.
Germany's air force operates 109 of the jets but of those 74 are in service and only 42 are ready for action.
The Bundeswehr had ordered 143 in a programme costing around €17 billion by 2018, according to estimates by the German military (Bundeswehr).
The Eurofighter is built by a consortium comprising European airplane maker Airbus, Britain's BAE Systems and Finmeccanica of Italy.
Germany and Britain had already halved their initial orders for 250 of the fighter jets each, and several export bids have fallen through, prompting the head of Airbus's defence division to say production could cease in 2018 if no more contracts came through.
In June, a Eurofighter crashed while coming into land in southwest Spain, killing its 30-year-old pilot. The cause was unknown.