Protecting the Naval forces from violent extremist organizations and individuals is one of NCIS' highest priorities. As the primary law enforcement and counterintelligence component for the Navy services, NCIS is focused on countering threats to the physical security of Sailors, Marines, and Department of the Navy civilian personnel and on preventing terrorist attacks against installations,  ships, and expeditionary forces.

NCIS is responsible for detecting, deterring, and disrupting terrorism worldwide through a wide array of investigative and operational  capabilities.  Within the Department of the Navy, NCIS has exclusive investigative jurisdiction into the actual, potential or suspected acts of terrorism.  NCIS accomplishes this through key partnerships resulting in enhanced information-sharing of threats to DON for forces and assets.  Offensive operations aim at identifying and interdicting terrorist activities. In defensive operations, NCIS supports key DON leaders with protective services and performs physical security assessments of military installations and related facilities—including ports, airfields, and exercise areas to which naval expeditionary forces deploy.