Authorities in the Bavarian town of Hammelburg have arrested a German soldier suspected of planning a terrorist attack against migrants, prosecutors and the Bundeswehr confirmed on Thursday.

The 28-year-old German national posed as a Syrian refugee in the states of Hesse and Bavaria in 2015 and early 2016, and later received state benefits and was put up in refugee accommodation despite speaking no Arabic, chief prosecutor Nadja Niesen said.

The man had been stationed as a Bundeswehr soldier in the French town of Illkirch and first appeared on the authorities' radar when he hid an illegal firearm at an airport toilet in Vienna several months ago, Niesen said.

He was temporarily arrested by Austrian police several days later as he was trying to retrieve the firearm, but was released.

Niesen told reporters that the man was suspected of planning to use the firearm to carry out a "serious act of violent subversion," but that investigators had not found evidence to suggest he had already chosen a target.

Some 90 police officers searched 16 locations in Germany, Austria and France on Wednesday in connection with the suspect, the prosecutor's office in Frankfurt said, adding that mobile phones, laptops and documents had been confiscated.

A 24-year-old German national was also arrested on Wednesday on suspicion of serving as an accomplice to the soldier. Authorities searched the student's flat and found weapons and "illegal items including a rocket flare," Niesen said.

The prosecutor described the case as "more than strange," adding that she had never before handled such a case.