“Based on the information published in the Egyptian media, the prosecution service… is investigating whether there are any indications of criminal offences,” the service in the city of Celle told AFP.
The 23-year-old student from the university town of Göttingen is one of two German men detained separately last month in Egypt, with an 18-year-old still in custody there on Friday.
The families of both men believe their arrests were cases of mistaken identity.
However, German public broadcaster SWR reported, without citing sources, that the 23-year-old was known to German police as a suspected Islamist. It said he had been the target of an investigation into the possible “planning of an act of violence against the state”.
Egyptian security sources said he was detained at Cairo International Airport over suspicions he was seeking to join the Islamic State group in Egypt's turbulent northern Sinai region.
Since had not committed any crime under Egyptian law, the authorities decided to deport to Germany, one of the sources said.
Germany's foreign ministry confirmed the return on Thursday of the man. It said its Cairo embassy was trying to gain consular access to the younger man, who was reportedly arrested in mid-December after landing in the southern city
The 18-year-old was found with maps of North Sinai in his possession and authorities believe he too came to Egypt with the intent of joining the Islamic State, Egyptian security sources said.
Procedures were still underway for his deportation to Germany.
Germany's foreign ministry said it could provide no information on the Egyptian accusation, nor whether they would be questioned in Germany.
Egypt has been battling an insurgency in North Sinai, which surged following the 2013 military ouster of Islamist president Mohamed Morsi.
In February, security forces launched a major operation focused on the region, aimed at wiping out an IS affiliate accused of spearheading the insurgency.