Interior Minister Nancy Faeser banned Compact magazine and the company that publishes it, Compact-Magazin GmbH, as well as a film production company, Conspect Film.
Police raided properties and apartments in four German regions linked to the organisations, their management and shareholders, her ministry said.
Faeser described Compact as "a central mouthpiece of the right-wing extremist scene".
She said "this magazine agitates in an unspeakable way against Jews, against people with a history of migration and against our parliamentary democracy".
"Our signal is clear: we will not allow who belongs in Germany and who doesn't to be defined by ethnicity," Faeser said in a statement.
Compact is run by far-right figure Jurgen Elsasser and produces the monthly magazine of the same name, which has a circulation of about 40,000, as well as an online video channel, Compact TV.
It also runs an online shop selling books, CDs, DVDs and other merchandise.
Compact has been published since 2010.
In its annual report for 2023, Germany's domestic intelligence agency said it "regularly disseminates ... anti-Semitic, anti-minority, historically revisionist and conspiracy theory content".
It said a main feature is agitation against parliamentary democracy in general and the German government in particular, and quoted Elsasser as saying on Compact's home page in 2023 that "we want to topple this regime".
The strength of the far right has caused increasing concern in Germany in recent months.
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