The 51-year-old official was said to have made a "partial confession" to the plot, according to Der Spiegel.
The suspect attempted to pass on "sensitive information about the BfV (Germany's domestic security agency), which could lead to a threat to the office", an official told the newspaper.
The BfV said the man "behaved inconspicuously" prior to his arrest. He had, since April, been engaged in gathering intelligence on Islamist extremists in Germany, Der Spiegel said.
Online chats were apparently found between the suspect and other Islamists in which he attempted to recruit them to the intelligence agency to mount an attack on "non-believers", carrying out a bomb attack on the spy HQ "in the name of Allah".
He used several different names online and his activities were uncovered about a month ago.