Schaeuble said: "The organisations are reservoirs of organised Holocaust deniers. Their activities include disseminating anti-Semitic propaganda and praising the tyranny of the Nazis over the internet, as well as in printed leaflets."
Authorities confiscated material siezed in searches of 30 premises in the various states early on Wednesday, the statement said.
Meanwhile, in the eastern state of Saxony, where the far-right National Democratic Party holds seats in parliament, a new report showed the party's membership in the state had dropped.
According to a state organisation that tracks extremism, the party lost 150 members in 2007, dropping to 850.
But the number of people belonging to an informal group that supported the National Democratic Party doubled to 500, said Albrecht Buttolo, the state interior minister.
Saxony reported an increase in crimes with a right-extreme background to 2,144 in 2007 over 2,063 in the previous year.
The rise was attributed to more confrontations with left-wing extremists.
Of those crimes, only 90 involved violence, up from 77 the previous year.
Saxony is the stronghold of the National Democratic Party, where it has the most members despite the recent drop.
It has been in parliament since 2004, when it won 9.2 per cent of the vote.