For the military side (Foreign Military Financing (FMF) and International Military Education and Training (IMET)), the State Department and the Defense Department control the disposition of funds provided to them by - Congress.
There are also Justice Dept, DHS, DEA and a whole host of other alphabet agencies providing funding for both classified and unclassified ventures. Congress controls all the funding. Oversight of the classified projects is limited to the members of Congress on the Intelligence Committees.
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