Choo Myeong-Ho, a former department head at the National Intelligence Service (NIS), is suspected of directing a string of operations to monitor and undermine high-profile figures and celebrities critical of then president Lee Myung-Bak and now ousted president Park Geun-Hye.
Choo was taken into emergency custody on charges of abuse of authority and political interference in violation of NIS law, the Seoul Central District Prosecutors' Office said, adding it will request a court warrant to arrest him formally.
A NIS internal investigation team has filed complaints with prosecution authorities, calling for Choo to face criminal charges.
The spy agency has been conducting a house-cleaning under the government of new President Moon Jae-In, who took office in May.