In April 1942, Coast Guard Air Station San Francisco was assigned to the operational control of the Commander, Western Sea Frontier, U. S. Navy. The Navy leased 85 acres at Mills Field and commissioned a Naval Auxiliary Airfield supporting Pan American which was flying under contract to the Navy. The Commanding Officer of the Coast Guard Air Station was also the Commanding Officer of the Naval Air Facility
The Station conducted Search and Rescue operations and commenced Coastal ASW Patrols. Coast Guard and Navy personnel flew joint ASW patrols in OS2U-3 Kingfisher aircraft. The station was also tasked with aiding in the construction of the highly classified and secret Long Range Navigation (LORAN) stations in the North Pacific during 1943. Four PB2Y-4 aircraft were assigned to provide personnel and material support for the LORAN program in the pacific.