Police spokesman Michael Merkle said officials were alerted to the theft at the sprawling site on Tuesday. He couldn't say how many taps were stolen, the Associated Press reported.
An investigation has begun into the theft, but police have so far found no signs of a break-in.
The incident is seen as embarrassing for the BND, as well as expensive, media reports say.
Merkle said Thursday that police have no information yet on who might be responsible, and haven't found traces of a break-in.
The Federal Intelligence Service, better known by its German acronym BND, is moving its headquarters from the Munich suburb of Pullach to the newly built complex in Berlin. The move is expected to be complete by 2017.