It said the man is believed to have headed the PKK (Kurdistan Workers' Party) in the west German cities of Mainz, Nuremberg and Darmstadt for three years, operating under the alias "Dersim" until mid-2007. From last summer, he is believed to have commanded the PKK cell in Berlin.
The suspect, who was identified only as Vakuf M., is likely to face charges of belonging to a banned organization and of kidnapping.
The second charge relates to an incident in which he is suspected of having helped members of the PKK's youth branch kidnap a renegade cadre and force the man to pay the organisation a large sum of money.
The PKK is considered a terrorist organisation by Turkey, the United States and the European Union and was banned in Germany - home to some 2.5 million people of Turkish origin - in 1993.
More than 37,000 people have been killed since it took up arms for self-rule in Turkey's mainly Kurdish east and southeast in 1984. Several suspected PKK militants have been extradited to Turkey from Germany in the past year.
Earlier this month, a presumed former lover of jailed PKK leader Abdullah Ocalan was arrested near the German border with Austria on charges of belonging to the separatist group.