The Berliner Morgenpost said the incident occurred in Kabul in 2002, in the latest of a series of revelations that have deeply embarrassed the country's military establishment.
The report to be published on Sunday said a German soldier had ordered the child into a patrol vehicle and out the loaded pistol to his temple, as colleagues took photographs.
"The kid was clearly frightened until he realised that he wouldn't be killed," it quoted the former NCO as saying, adding that he had been given a dollar and allowed to go.
A defence ministry spokesman said on Saturday, "We ask those who are making these assertions to give us the proof so that we can investigate quickly."
Twenty-three soldiers are already under investigation for alleged desecration of human skeletons in Afghanistan, and six have been suspended.

Copyright AFP (Agence France-Presse), 2006