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Cost

The project expenditure through 1 October 1945 was $1.845 billion, equivalent to less than nine days of wartime spending, and was $2.191 billion when the AEC assumed control on 1 January 1947. The total allocation was $2.4 billion. 84% of the costs through the end of 1945 were spent on the plants at Oak Ridge and Hanford, producing the enriched uranium and plutonium needed to fuel the bombs. At both sites, the majority of the costs were for construction (74% at Oak Ridge, 87% at Hanford), with the rest being for operations.

Initial funding for the project was through the general budget of the Office of Scientific Research and Development. As plans were made to turn the work over to the Army Corps of Engineers, Bush wrote to Roosevelt in late 1942 that "it would be ruinous to the essential secrecy to have to defend before an appropriations committee any request for funds for this project." Instead, initial funding was done through discretionary funds to which Roosevelt had access.

As it grew in size and cost, Congress was deliberately kept ignorant of the project, because of concerns that Congressmen were prone to leaking information, and because it was feared that the project would appear to be a boondoggle. Appropriations requests were quietly slipped into other bills, but the project's mounting costs and large facilities (which appeared to many to produce nothing) attracted scrutiny from several Congressional auditors. The Truman Committee that investigated wartime waste and fraud attempted to audit the project several times, but each time their inquiries were rejected.

These Congressional inquiries, along with the need for smooth budgetary approval, led to Bush, Groves, and Stimson agreeing in the spring of 1944 that a few high-ranking Congressmen should be told of the project's purpose. By March 1945, exactly seven Congressmen were officially informed. The funds were hidden into appropriation requests with the inconspicuous headings, frequently "Engineer Service Army" and "Expediting Production." In late May 1945, to further expedite budget issues and assure the cooperation of Albert J. Engel, who had threatened to reveal the existence of the project if he was not told more about it, five additional Congressmen were permitted to visit the Oak Ridge site to assure themselves of "the reasonableness of the various living accommodations which had been provided, that they actually observe the size and scope of the installations and that some of the complexities of the project be demonstrated to them."

During the war, the Manhattan Project ultimately produced the three bombs used (the Trinity gadget, Little Boy, and Fat Man), as well as an additional unused Fat Man bomb, making the average wartime cost per bomb around $500 million in 1945 dollars. By comparison, the project's total cost by the end of 1945 was about 90% of the total spent on the production of US small arms (not including ammunition) and 34% of the total spent on US tanks during the same period. It was the second most expensive weapons project undertaken by the United States during the war, behind only the Boeing B-29 Superfortress.