The groups "have established themselves in north Africa without being detected and are reinforcing the network of Osama bin Laden," Ernst Uhrlau, head of the BND intelligence agency, told German weekly news magazine Der Spiegel, in a special edition.
"The BND is monitoring with great concern...what is growing over there, which has a new quality and is bringing the jihad (or holy struggle) to our door," he said.
Deputy interior minister August Hanning warned in October of "movements" or "communications" between Islamists in north Africa and Germany. He also raised concern about alleged extremist camps in northern Mali.
It is in this African region where kidnappers are suspected of holding two Austrian tourists abducted last month in Tunisia. Efforts are ongoing to secure their release.
In Germany, some 700 people are under surveillance by intelligence agencies, Uhrlau said in the Spiegel interview.
More than a dozen suspects, including Germans who converted to Islam, are believed to have gone to training camps in Afghanistan and Pakistan, he said.