According to the report, new recruits to the army ambulance service were subjected to violence, humiliation and sexual assault by their superiors.
"Internal and hitherto secret investigations have confirmed that in the training of paramedics, or 'Combat First Responder,' sexually sadistic practices were apparently the order of the day. Investigations have also revealed abject ritual violence among sentries at the barracks," the magazine reported.
The investigation began in October 2016 when a female lieutenant raised the alarm with the Parliamentary Commissioner for the Armed Forces, Hans-Peter Bartels.
She described abuse during the training of ambulance recruits at Pfullendorf. For example, recruits were forced to strip naked in front of their colleagues, who filmed them.
She also said that army instructors had forced them to carry out unnecessary and sexually abusive exercises such as the insertion of tampons into the anus of male and female recruits, which was also photographed.
Sources in the Bundeswehr told Der Spiegel that indications of poor training practices and harassment of women first came to light in 2015, but were dismissed by the leadership at the barracks.
Commander of the barracks, Colonel Thomas Heinrich Schmidt, and two officers and two sergeants have been moved to positions away from the barracks, "to enable a new beginning."
"This series of events shows serious deficits in leadership," a Bundeswehr source said.
"The ministry is shocked by the results of the investigation. In addition to the shocking practices at medical training, it also became apparent that bizarre humiliation rituals were the order of the day among soldiers."
"The soldiers bound each other to chairs, had to stand for hours and were hosed with water. They also recreated scenes from the Hollywood film 'A Few Good Men,' and regularly took photos," the German newspaper wrote.
The allegations come as an embarrassment to von der Leyen, who has tried to promote a better image for the German army with a multi-million euro PR campaign to attract new recruits.
The issue will be discussed by von der Leyen and senior military figures at a conference on Tuesday. German media noted that the forum is called "Sexual orientation and identity in the Bundeswehr," and had actually been planned to highlight the army's modernization.
However, the conference is now set to be dominated by concerns about the extent of physical and sexual abuse at army barracks in Germany, with new cases expected to come to light as the investigation continues.