The soldier, who has been named as "Franco A" was detained after he attempted to retreive a loaded pistol he had stashed in a bathroom in Vienna International Airport.
A German soldier, suspected of planning a terrorist attack, was arrested on Thursday, a prosecutor said.
The German Interior Ministry admitted on Friday that "mistakes were made" in the case of a 28-year-old soldier who was able to fool authorities and register as a Syrian asylum-seeker and receive financial aid.
"Based on the current investigation the prosecutor's office believes, or has at least suspicions, that the accused soldier had possibly planned to carry out a severe act of violence in terms of an attack with the weapon stored in Vienna", prosecutor Nadja Niesen said at a press conference.
The lieutenant was not only planning to disguise himself as a refugee but had also falsely registered himself as a refugee to bolster the story that the attacker was a refugee. Shortly afterwards in January of past year, the officer, whose name has been withheld, applied for asylum in Bavaria and was allocated a room at a local refugee facility. "Just because he was stationed in France, it does not mean that he was there every day".
"He is believed to have posed as a Syrian war refugee at the end of December 2015 using a false name".
The case is now being handled by the prosecutor's office in Hessen, the Federal Criminal Police Office (BKA) and the military counterintelligence service.
Nadia Niesen of the Hessen prosecutor's office said he may also have had a 24-year-old accomplice.
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.
"Investigators must clearly and carefully examine how a Bundeswehr soldier could have his application as a Syrian asylum seeker recognised", he added. They found several items banned under weapons and explosives laws at his home in Offenbach, near Frankfurt in the south of Germany.
At least two neo-Nazi terror plots have been uncovered, while security services have cracked down on the anti-government Reichsbürger movement after one of its members killed a police officer. He now faces charges of plotting a terrorist attack, fraud and violation of gun laws.