NAVFAC Headquarters (HQ) is an Echelon II Systems Command (SYSCOM) reporting to the Chief of Naval Operations (CNO) through the Vice Chief of Naval Operations (VCNO). NAVFAC receives acquisition authority from the Assistant Secretary of the Navy for Research, Development, and Acquisition (ASN RD&A) and real estate authority from the Assistant Secretary of the Navy for Energy, Installations and Environment (ASN EI&E).
NAVFAC Atlantic (LANT), NAVFAC Pacific (PAC), NAVFAC Engineering and Expeditionary Warfare Center (EXWC), and the Navy Crane Center (NCC) are Echelon III Commands and report to NAVFAC HQ. The Echelon IV Commands report to LANT and PAC, respectively. NAVFAC EURAFSWA is an Echelon IV Command and reports to NAVFAC LANT.