Secretary of the Navy Instruction 3850.2E defines counterintelligence as "information gathered and activities conducted to identify, deceive, exploit, disrupt, or protect against espionage, other intelligence activities, sabotage, assassinations conducted for or on behalf of foreign powers, organizations, persons, or their agents, or international terrorist organizations or activities. " (SECNAV Instruction 3850.2E, January 3, 2017).

Within the Department of the Navy, NCIS serves as the coordinating authority of all DON CI activities, and is the only Department of Navy (DON) Component authorized to conduct investigations into actual, potential or suspected acts of espionage, sabotage, and intelligence activities conducted on behalf of foreign powers.  NCIS is also DON lead agency for the conduct of offensive CI operations, which seek to penetrate and neutralize adversary intelligence services. 

NCIS works to neutralize foreign intelligence services and foreign commercial activities seeking information about critical naval programs and research, development, test and evaluation facilities. The Research and Technology Protection (RTP) program works to safeguard the nation's vital defense technology through engagement and partnering with security and intelligence agencies.