DawaFFM, Islamische Audios and An-Nussrah all adhere to ultra-conservative Salafist doctrine.
Police mounted raids against the groups on Wednesday, but no arrests were made.
German officials have said videos produced by DawaFFM partly inspired the man who shot dead two US airmen at Frankfurt airport in 2011.
An-Nussrah was judged to be part of the Millatu Ibrahim organisation, which had been banned in June last year.
"Salafism, as represented by the groups banned today, is incompatible with our peaceful, democratic system," Interior Minister Hans-Peter Friedrich said in a statement. [BBC] Read more
