Lower Saxony state police say the man, identified only by the initial 'M', was arrested on Wednesday at a refugee center in the central city of Giessen.
Police said the man's fingerprints had been linked to the capture of the Marida Marguerite and its 22 crew off the coast of Oman.
The Somali pirates allegedly tortured their captives for seven months before receiving "several million dollars' ransom."
According to today's German police statement, the man was in charge of doling out the ransom money and supplying the ship with food.