1956-1958 Capt. George T. Gregory
Capt. Gregory took over as Blue Book's director in 1956. Clark writes that Gregory led Blue Book "in an even firmer anti-UFO direction than the apathetic Hardin." The 4602nd was dissolved, and the 1066th Air Intelligence Service Squadron was charged with UFO investigations. In fact, there was actually little or no investigation of UFO reports; a revised AFR 200-2 issued during Gregory's tenure emphasized that unexplained UFO reports must be reduced to a minimum. One way that Gregory reduced the number of unexplained UFOs was by simple reclassification. "Possible cases" became "probable", and "probable" cases were upgraded to certainties. By this logic, a possible comet became a probable comet, while a probable comet was flatly declared to have been a misidentified comet. Similarly, if a witness reported an observation of an unusual balloon-like object, Blue Book usually classified it as a balloon, with no research and qualification. These procedures became standard for most of Blue Book's later investigations.
1958-1963 Major Robert J. Friend
Maj. Friend was appointed the head of Blue Book in 1958. Friend made some attempts to reverse the direction Blue Book had taken since 1954. Jerome Clark writes that "Friend's efforts to upgrade the files and catalog sightings according to various observed statistics were frustrated by a lack of funding and assistance." Heartened by Friend's efforts, Hynek organized the first of several meetings between Blue Book staffers and ATIC personnel in 1959. Hynek suggested that some older UFO reports should be reevaluated, with the ostensible aim of moving them from the "unknown" to the "identified" category. Hynek's plans came to naught. During Friend's tenure, ATIC contemplated passing oversight Blue Book to another Air Force agency, but neither the Air Research and Development Center, nor the Office of Information for the Secretary of the Air Force was interested. In 1960, there were U.S. Congressional hearings regarding UFOs. Civilian UFO research group NICAP had publicly charged Blue Book with covering up UFO evidence, and had also acquired a few allies in the U.S. Congress. Blue Book was investigated by the Congress and the CIA, with critics—most notably the civilian UFO group NICAP_ asserting that Blue Book was lacking as a scientific study. In response, ATIC added personnel (increasing the total personnel to three military personnel, plus civilian secretaries) and increased Blue Book's budget. This seemed to mollify some of Blue Book's critics, that but it was only temporary. A few years later the criticism would be even louder. By the time he was transferred from Blue Book in 1963, Friend thought that Blue Book was effectively useless and ought to be dissolved, even if it caused an outcry amongst the public.
1963- Major Hector Quintinilla
Maj. Quintanilla took over as Blue Book's leader in August 1963. He largely continued the debunking efforts, and it was under his direction that Blue Book received some of its sharpest criticism. UFO researcher Jerome Clark goes so far as to write that, by this time, Blue Book had "lost all credibility." Physicist and UFO researcher Dr. James E. McDonald once flatly declared that Quintanilla was "not competent" from either a scientific or an investigative perspective. However, McDonald also stressed that Quintanilla "shouldn't be held accountable for it", as he was chosen for his position by a superior officer, and was following orders in directing Blue Book. Blue Book's explanations of UFO reports were not universally accepted, however, and critics — including some scientists — suggested that Project Blue Book was engaged in questionable research or, worse, perpetrating a cover-up/ This criticism grew especially strong and widespread in the 1960s.