The spy agency official, only known by his surname Kim, was arrested a day earlier upon the issuance of an arrest warrant from a Seoul court, the Seoul Central District Prosecutors' Office said.
He is now under interrogation, it said.
Kim has been at the center of the snowballing scandal over the National Intelligence Service, (NIS) which has allegedly attempted to frame a North Korean defector for espionage.
Charges against Kim include forging and using fake documents in his pursuit of the espionage case.
The case involves Yoo Woo-seong, a 34-year-old defector, who was indicted on charges of relaying to North Korean intelligence a list of North Koreans who defected to the South and their personal information while he was working for the Seoul municipal government.
A local court, however, acquitted Yoo of the espionage charges in August 2013, and allegations have risen that the NIS has used fake immigration documents to bring the espionage case against Yoo. (Yonhap)