I think this is true: discussion of improving management in government, particularly IT, stumbles on a simple fact of terminology--much of the literature uses "agency" to mean "department" (because they also want to include the independent agencies, and "department-level" or similar wording seems too awkward). See this discussion of IT management. The problem is that it leads to the easy assumption that the "agency" is a cohesive unit, where the agency head and her CIO can control the operations of the agency's components.
For USDA, and I suspect at other government departments, the idea of the "agency" as being cohesive and under the direction of the Secretary and his CIO is laughable. Even after the reorganization of the department in the Clinton Administration, there's a bunch of agencies which do not snap to when the Secretary yells: "attention". Just ask ex-Secretary Glickman about his efforts to do some integration of NRCS and FSA.