Jung said following “much consideration” he would step down one day after the Bundeswehr's Chief of Staff Gen. Wolfgang Schneiderhan resigned for allegedly withholding information about a bombardment that ended in dozens of civilian casualties.
"I am therefore taking the political responsibility for the internal information policy of the Defence Ministry regarding the events of September 4 in Kunduz," he said in Berlin. "With this action, I would like to help the federal government continue without hinderance its successful work and avert damage to the Bundeswehr."
Two days after a German colonel called the air strike on two fuel trucks hijacked near the northern Afghan city of Kunduz, Jung had said that according to his information "only Taliban terrorists" were killed.
However, a confidential NATO report cited by Schneiderhan in late October said that the death toll could be as high as 142 and local sources claimed between 30 and 40 civilians had died.
But the ministry allegedly hushed up another report regarding civilian casualties which suggested the military commanders on the ground did not adhere to the agreed rules of engagement.
After chief of staff General Wolfgang Schneiderhan stepped down on Thursday, the clamour for Jung's head had grown even louder. Chancellor Angela Merkel conspicuously failed to ride to her minister's aid, saying only that full transparency was crucial to the increasingly unpopular mission in Afghanistan.
Jung, not seen as a particularly close ally of the chancellor, had been moved to his new post at the Labour Ministry after Merkel was re-elected two months ago.
In a devastating front-page editorial entitled "Resign Please," the Financial Times Deutschland on Friday said: "Franz Josef Jung failed as defence minister and should resign from his position as labour minister. It would be no loss to the cabinet. There's nothing more to say."
The paper left the rest of its front-page editorial column blank in a stark visual statement.
Merkel said late on Friday she had appointed Family Minister Ursula von der Leyen to replace Jung at the Labour Ministry. The ministerial duties of 51-year-old mother of seven will be taken over by Kristina Köhler, Merkel told reporters.
In a short statement, Merkel also said she had the "greatest respect" for Jung's decision to step down.