Von der Leyen, who has blasted "weak leadership" across the military, told her top 100 generals and admirals to come to Berlin on Thursday to discuss the latest case involving a first lieutenant and several sexual assault and harassment scandals.
"We have to ask systematically how someone with such clear right-wing extremist views, who writes a master's paper with clearly nationalistic ideas ... could continue to pursue a career in the Bundeswehr," von der Leyen told reporters.
According to Reuters, she said it was important to address the "burning questions" of "where leadership and accountability have failed ... and why" but warned that the process could take weeks and months.
Germany's chief federal prosecutor's office on Tuesday took over the case of the 28-year-old lieutenant and a 25-year-old student from state prosecutors, citing "preliminary indications of preparations for a serious attack against the state".
A spokesman told Reuters TV that investigators were examining materials seized during searches last week to determine if other people were also involved.
Von der Leyen, a member of Chancellor Angela Merkel's conservatives who is often named as a possible Merkel successor, had been due to meet with U.N. officials and U.S. Defense Secretary Jim Mattis in New York and Washington this week.
Von der Leyen said she would travel to Illkirch, the French town south of Strasbourg where the officer was stationed with a German army brigade, on Wednesday for an update on the probe.
Some politicians pushed back against the minister's sweeping criticism of the military for which she is responsible.
"She cannot and should not .... claim the position of a neutral observer," Lorenz Caffier, a fellow conservative, interior minister of the state of Mecklenburg-Vorpommern and a reserve officer, told the RND newspaper chain.
Henning Otte, a conservative lawmaker and head of the parliamentary defence committee, told Reuters the military had "no fundamental problem with radicalism or abuses".
However, Germany's MAD military intelligence agency reported last month that there had been 275 suspected case of right-wing extremists in the military's ranks, including some dating back to 2011 and 53 cases first identified this year.
Von der Leyen emphasized that it was a minority of leaders who had failed to punish bad behavior in the recent cases, but that most military officers took their responsibilities seriously.
Still, she said, "if I look at the patterns, then I think I should have dug deeper earlier."
XENOPHOBIC VIEWS
German police last week arrested the first lieutenant, who had falsely registered as a Syrian refugee in January 2016, and also detained a 24-year-old student who was found to possess explosives. Prosecutors said that both men harbored "xenophobic views".
Tagesspiegel newspaper said the soldier, identified by prosecutors only as Franco A., had a list of five possible targets for attacks, including former German President Joachim Gauck and Justice Minister Heiko Maas.
Von der Leyen said investigators were looking at the environment in Illkirch, citing evidence found of Nazi swastikas and photographs of Nazi-era soldiers. The Sueddeutsche Zeitung newspaper also reported late on Tuesday what it called "indications of the possible theft or loss of munitions."
The federal prosecutor's office had no immediate comment on either report.
The bizarre case surfaced days after von der Leyen fired another top officer who had overseen the military's training command, in the wake of a sexual hazing and harassment scandal at a training base.