Many of these decisions are made by Congress, not DOE. As part of the President's Budget submission, DOE submits a budget proposal to Congress. Congress then goes through that budget. As part of their Constitutional duties, Congress frequently says "you're spending too much money here, not enough there." Congress passes the budget, and the President generally signs it. DOE is then stuck with the budget it is given. While DOE has some discretion in moving money around because of unforeseen circumstances, it does not have a free hand. Furthermore, frequently through the committee reports, Congress provides "guidance." In essence saying, "We, the Congress, put this money here for a reason, you better not move it, or there will be hell to pay." Federal agencies pay a lot of attention to "Congressional language." Furthermore, there is a problem in DC known as the "color of money." Congress puts money into different accounts. Frequently, the law says this color of money (e.g., money for salaries) cannot be used for other things (e.g., building new buildings). Added all together, there is a limit on what federal agencies can do.