Regional Joint Terrorism Task Forces (JTTFs) were initiated in 1980 by the FBI in an interagency approach to combatting terrorism. NCIS has Special Agents and analysts integrated into 22 FBI-led JTTFs around the United States, positioned where the Department of the Navy's equities are greatest. In addition, NCIS has a presence at the National Joint Terrorism Task Force, which oversees the regional JTTF network.

The primary focus of the JTTFs is to investigate and thwart terrorist threats to the United States. By pooling the competencies and resources of federal, state and local law enforcement agencies and elements of the United States Intelligence Community into joint interagency teams, the JTTFs are able to draw upon a wide array of knowledge, talent and experience to help protect the American people.