By Ben Farmer in Kabul
The military's inspector general asked to be relieved of his duties after a newspaper reported the military knew civilians had died even as German ministers were denying the allegation.
In the days after the Afghan strike Germany denied there had been any civilian victims. (Photo: EPA)
A Nato inquiry has since said up to 142 people including civilians died in the September 4 bombing of two hijacked fuel tankers in Kunduz province.
A German colonel ordered the air strike fearing the Taliban would use the tankers in a suicide attack on a nearby German base.
Reports of civilians casualties soon emerged with villagers saying the lorries had been surrounded by locals collecting fuel at the time of the strike by US jets.
Two days after the attack, Franz Josef Jung, then defence minister, was still insisting that according to his information "only Taliban terrorists" were killed.
However a report in Bild said the German military had already received reports and video showing civilians had probably died.
Only hours after the strike, commanders in Afghanistan had informed headquarters in Potsdam, that there were two dead teenagers in Kunduz hospital as well as six people injured "aged between 10 and 20".
A German military doctor also reported that there were two boys "aged around 14" with "open wounds" and "shrapnel injuries", the paper reported.
Karl-Theodor zu Guttenberg, current defence minister, told the German parliament on Thursday that Gen Schneiderhan "has released himself from his duties at his own request."
He added: "State secretary (Peter) Wichert is also taking responsibility."
Mr Guttenberg said he had only been made aware of the evidence on Wednesday. It was not clear if Mr Jung, now Labour minister, had seen the evidence.
Germany is the third biggest contributor to the Nato-led mission in Afghanistan and its 4,300 troops have this year found themselves facing a new Taliban "northern front".
German commanders believe their contingent is being specifically targeted as a weak link in the coalition because of strong domestic opposition to the deployment.