It is under scrutiny over allegations of abuse, the discovery of suspected far-right extremists in its ranks and questions over its ability to fulfil its missions.
In a pre-recorded video yesterday, Merkel said "there were events recently that deserved to be criticised."
But she insisted that "the vast majority of soldiers are performing an invaluable service."
Defence Minister Ursula von der Leyen angered some in the military with her sweeping criticism while investigations into alleged wrongdoing were still underway.
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