Eleven of the men, arrested in country-wide raids in February, stand accused of membership of a terrorist organisation and weapons law violations. The 12th has been charged with supporting a terrorist group.
The federal prosecutor's office could not immediately be reached for comment.
The arrests followed raids, some by heavily-armed special units, which hit 13 locations in six German states.
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The four prime suspects planned to spark “a civil-war-like situation… via as yet undefined attacks on politicians, asylum seekers and people of Muslim faith,” federal prosecutors said in February.
The suspects are believed to have founded a “right-wing terrorist organisation” with the goal of “destabilising and ultimately overthrowing” Germany's democratic order.
A further eight suspects were alleged to have agreed to “financially support the group, provide it with weapons or take part in future attacks”.
In order to plan their attacks, the group allegedly held regular meetings which were coordinated and organised by two of the main suspects, named only as Werner S. and Tony E.
The suspects, all of whom are German citizens, also communicated using messenger apps.
German authorities have increased attention paid to the country's underground extreme right scene since the murder of conservative local politician Walter Lübcke in June 2019 and an attack on a synagogue in the eastern city of Halle in October last year.
Media reports said police discovered several weapons in the February raids, including one self-made “slam gun” similar to the one used in the Halle attack.
Interior Minister Horst Seehofer announced late last year 600 new posts across the federal police and domestic security services to track far-right extremist threats, citing a growing danger.