Hans-Peter Friedrich told Die Welt newspaper that in mid-September, 110 far-right extremists who should be in jail were missing – living in hiding somewhere in the country.
His interior ministry asked all of the 16 German states to provide figures for how many arrest warrants had been issued on neo-Nazis.
A tally is made every six months, but no follow-up information is recorded – for instance if the suspect is taken to court, the outcome is not always added to a person's file, Der Spiegel magazine said on Saturday.
This needed to improve, said Friedrich, who is pushing for better communication between national and state intelligence services. He added that this included closer communication between criminal police investigators and news organisations.
Domestic intelligence agencies and the police have come under serious criticism since the neo-Nazi terrorist cell calling itself the National Socialist Underground was unveiled – having allegedly killed ten people over a period of years.
Friedrich said he was not expecting copycat attacks, despite the 110 wanted neo-Nazis being free.