NCIS was aligned as an echelon two activity under the Secretary of the Navy, via the General Counsel.

[3] In May 1997, David L. Brant was appointed director of NCIS by Secretary of the Navy John Howard Dalton.

On February 14, 2010, Mark D. Clookie became the fourth civilian director of NCIS, having been appointed to the position by Secretary of the Navy Ray Mabus.

[4] On October 7, 2013, Andrew L. Traver became the fifth civilian director of NCIS, having been appointed to the position by Secretary of the Navy Ray Mabus.

On June 4, 2019, Omar R. Lopez became the sixth civilian director of NCIS, having been appointed to the position by the Secretary of the Navy, Richard V.