Security Agency (NSA) was created not by an act of Congress but instead by an executive order issued by President Truman in 1952. The very existence of the NSA was classified for over two decades, even though it spent hundreds of millions of dollars over that span; its funding was hidden in the federal budget under various cover names and in the funding for non-secret agencies such as the Central Intelligence Agency. Likewise, the National Reconnaissance Office (NRO) was created by President Eisenhower in 1960 with another executive order. The NRO coordinated the operations of America's spy satellites and the processing of intelligence gathered by them, yet its existence remained classified until 1994 (even the term National Reconnaissance Office was classified until then). A congressional audit after the existence of NRO was disclosed revealed that NRO had spent over $4 billion since its founding that could not be accounted for.
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Congressional investigators did not feel this was the result of sloppy management, bad accounting, or fraud; instead, it was believed that money had been diverted to”as difficult as it may be to imagine” even more highly classified programs and agencies.
It is highly likely there are other agencies of the scope and power of the NSA and NRO operating today that are just as highly classified as those two once were.
Several overt government agencies had classified components during the 1950s and 1960s. For example, the Office of Civil Defense ran many public programs encouraging people to build fallout shelters, stockpile emergency supplies, and coordinated state and local plans for dealing with nuclear war. But at the same time it also developed and administered a plan known as Continuity of Government, whose aim was to protect as many high federal officials as possible in the event of a nuclear attack. In great secrecy, underground shelters capable of housing thousands of government officials (including the entire U.S. Congress) were built near Washington, DC. A variation of the Continuity of Government is carried on today by the Federal Emergency Management Agency, and some senior government officials (such as Vice President Dick Cheney) were taken to those underground shelters in the first hours after the September 11, 2001 attacks. It is likely that similar classified activities go on today in publicly-known government departments and agencies.