Two days after the raid, which took place on September 4, Jung said that "only Taliban terrorists" had been killed in the incident.
But the Afghan government found that 69 Taliban fighters and 30 civilians had died, while a report by the Nato military alliance said the air raid killed between 30 and 40 civilians, as well as a number of fighters.
Army chief's exit
General Wolfgang Schneiderhan, Germany's highest-ranking soldier, and Peter Wichert, a senior defence ministry official, stepped down on Thursday following the Bild allegations.
Polls show Germany's role in Afghanistan is increasingly unpopular at home [EPA]
Angela Merkel, the German chancellor, had conspicuously failed to ride to Jung's aid following the resignations, saying only that full transparency was crucial to win confidence in the Afghan mission.
In a devastating front-page editorial entitled "Resign Please", the Financial Times Deutschland said: "Franz Josef Jung failed as defence minister and should resign from his position as labour minister."
It said: "It would be no loss to the cabinet. There's nothing more to say."
Handelsblatt, a business daily, said: "The man is out of his depth. No doubt about it, he has to go."
Smelling ministerial blood just weeks after Merkel formed her new cabinet after her crushing election victory, opposition parties also piled in with vigour.
"Mr Jung is not suitable for a government position," said Susanne Kastner, chair of the defence committee in Germany's parliament and a member of the main opposition party, the Social Democrats.
Hans-Christian Stroebele, a senior Green party politician, told the Berliner Zeitung newspaper it could not be the case "that the defence ministry is some sort of madhouse where the top people don't know what's being reported in Afghanistan".
Germany has about 4,500 soldiers serving in Afghanistan and polls show the mission is becoming increasingly unpopular at home.