The number of investigations into Islamic terrorism in Germany, where the 9/11 attacks on the United States were planned, has risen continually since 2001 according to the BKA. A total of 352 investigations were now under way, they said.
"Security officials in Germany believe there are more than 1,000 Islamists ready to commit violence," the BKA, a nationwide police agency, said in a statement for its autumn congress.
Authorities in the European Union's most populous state had classified 131 Islamists in Germany as "instigators" of terrorism and held files on a further 274 individuals deemed relevant, the BKA said.
Radical Islam has been under the spotlight in Germany again over the past few weeks since security officials said a plot to stage attacks in Europe had been disrupted thanks to information from a suspected German militant captured in Afghanistan.
Recent reports suggest a rise in Islamic militancy could be occurring in tandem with an increase in xenophobia.
A study by the Friedrich Ebert Foundation, which is close to the centre-left opposition Social Democratic Party (SPD), showed 58 percent of those surveyed said Muslims' rights to practise their religion in Germany should be considerably limited.
The group agreeing with the statement "I don't like Arabs" rose from 44 percent in a 2003 poll to 55 percent this year, the study said. It also showed opinions once limited to the neo-Nazi scene were now spreading across German society more widely.
The BKA said potential for far-right violence had almost doubled from the 1990s on, and encompassed around 9,000 people.
Germany has been engaged in a very public debate about its Muslim population following a spate of disparaging remarks about immigrants made by Bundesbank board member Thilo Sarrazin.
Sarrazin was later removed from office, but a book he wrote addressing the role of immigrants has become a best-seller.
In what has been widely perceived as a sharp shift to the right on the issue, Chancellor Angela Merkel said at the weekend that multiculturalism had "utterly failed" in Germany.