Maximilian T, 27, was arrested in the southwestern city of Kehl on charges of preparing an act of violence, federal prosecutor's spokeswoman Frauke Koehler said.
His apprehension follows the arrest last month of 28- year-old Lt Franco A, a Bundeswehr soldier stationed with a Franco-German brigade in Illkirch, just across the border from Kehl in France. Their last names weren't released in line with privacy laws.
Though stationed with the Bundeswehr in France, he lived sporadically at the refugee home and T is alleged to have covered him, at times, when he was absent from the barracks, prosecutors said.
A. Came to the attention of authorities after he was arrested in February while going to retrieve a pistol he'd stashed in a Vienna airport bathroom. He was freed, but Austrian authorities informed Germany, and when the soldier's fingerprint matched the one he'd given when he registered as a refugee, it triggered the current investigation.
Koehler said the three are believed to have been planning to attack "high-ranking politicians and public figures who, in the eyes of the suspects, engaged in failed refugee policies."
Among others on a list they put together were former German President Joachim Gauck, and Justice Minister Heiko Maas, she said.
A was to carry out the attack under his "fictitious identity" as a Syrian refugee, Koehler said.
"In this way the three suspects wanted to link the attack in Germany to asylum seekers," she said.
Defence Minister Ursula von der Leyen canceled a visit to the US after the case broke, and met with top members of Germany's military last week to try and determine where mistakes were made.
Among other things, A came to the attention of superiors for expressing what von der Leyen called "clearly racist and far-right extremist" views in a 2014 dissertation written as part of his officer's training, but was let off with a warning.
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