The federal government also operated a number of bases that continued during World War II and were subsequently decommissioned. The Clearfield Naval Supply Depot officially opened in April 1943. The mission of the depot was to provide a reservoir of materal in support of West Coast supply points and the advance bases of the Pacific Fleet. The Depot was also used as a depository for the personal effects of men lost in action, and housed a sizable German prisoner-of-war camp. The depot's workload declined between wars until the facilities were transferred to General Services Administration in 1962. A number of industrial and governmental enterprises have moved to the depot to take advantage of the rental storage space available. Perhaps the most regrettable incident of Utah's war years was the country's widespread prejudices against American citizens of Japanese ancestry that prompted the deportation of citizens and aliens of Japanese ancestry to relocation centers in the west. One was located at Topaz, in Millard County. Topaz was an enclosed city of barracks with limited freedoms and facilities; it operated from September 1942, until October 1945.

Other temporary installations during World War II, included the Bushnell General Hospital near Brigham City and Kearns Air Base in Salt Lake County. Bushnell served as a facility for treatment of severely wounded military personnel. Kearns functioned primarily as a training field for Air Corps personnel. Following the war, Bushnell was turned over to the Bureau of Indian Affairs and became the Intermountain Indian School. By the spring of 1943, Kearns had grown until it was Utah's third largest city, boasting a military population of 40,000 troops. By October 1943 Kearns facilities had trained over 90,000 airmen. The base continued to function until the end of World War II when the War Assets Administration declared the camp surplus. The "surplus" townsite became one of Utah's fastest growing communities.