The 28-year-old lieutenant, whose name wasn't released, faces charges of preparing an act of violence, Frankfurt prosecutor's spokeswoman Nadja Niesen told reporters.
The officer, who was "of German background" and stationed in France, allegedly stashed a loaded pistol in a bathroom at the Vienna airport that was discovered, leading Austrian authorities to take him into temporary custody when he went to retrieve it in February, Niesen said.
A 24-year-old student from the soldier's hometown of Offenbach was also arrested.
"We know from various voice recordings that both had anti-foreigner views," Niesen said.
The officer had registered as a Syrian refugee in the state of Hesse at the end of 2015 and had been living "sporadically" at a home for asylum seekers on and off since January 2016. Though he was officially stationed with the Bundeswehr in 2016, authorities say he wasn't required to be present at all times.
"It sounds more than strange," Niesen said. "I think we have to await more from the investigation to find out more about his motivation."
Sixteen buildings were searched in Germany, Austria and France in connection with the investigation, and multiple mobile telephones and other electronic devices were seized as evidence, Niesen said.
Niesen said the suspect knows no Arabic and she did not know how he managed to pass himself off as a Syrian refugee.
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