Well, having now had some time to digest what Vallee notes in his journals, what to make of it?
So, analysts in both the CIA and NSA did indeed monitor the subject. The FOI output of documents from these organisations supports these observations of Vallee's.
However, Vallee states that neither agency set up a serious research project into the phenomenon, instead any work done was at the individual level of personal interest.
The CIA worried about what the military knew. While private industry in the form of McDonnell-Douglas conducted research.
I guess the bottom line to draw from this look at the 1970's is that Vallee, who was certainly well connected enough to know these things, says there was no serious scientific research project.
According to the work conducted by the Disclosure Australia project, the same thing happened here. Harry Turner who worked for the Joint Intelligence Bureau, now the Defence Intelligence organisation, appeared to be working out of personal interest, but with the knowledge of his superiors. The JIB/JIO file located by Keith Basterfield clearly shows this fact. Turner's boss saw there was something to the UFO phenomenon, but declared it was not their role to look into it.
All in all Vallee's latest work clarifies a few things in this intelligence arena. A good read.