Defence Minister Karl-Theodor zu Guttenberg on Friday said that mistakes were made in a German-ordered air raid in northern Afghanistan on September 4 in which as many of 142 people may have died.
But he insisted that the bombing by US aircraft ordered by a German commander was "military appropriate", saying: "Even if there had been no procedural errors, the raid should still have taken place."
Guttenberg, appointed defence minister last month, replacing Franz Josef Jung, said in Berlin that he believed that there had been civilian casualties, adding that he "deeply regrets every civilian death".
Germany's Colonel Georg Klein ordered the strike after insurgents hijacked two trucks carrying fuel which then got stuck in a river bed.
A report by NATO said between 17 and 142 people perished.
Germany has around 4,300 troops in an increasingly unpopular mission in Afghanistan facing an ever more tenacious insurgency.
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