Wouldn't most of these follow secret government projects and not secret societies? While secret societies could definitely exist and even thrive inside of goverment operation, the operation itself doesn't constitute as a society. These are people that are employed to do a job by the government and the institution itself is kept confidential by that same government.
A secret society is autonomous to the greater society it exists within. Members are not employed but offered acceptance, and more than likely have to contribute financially or some other way to the whole as opposed to working and getting paid for their services. Thus, I think government operations should be excluded as something else entirely.
I do, however, believe that secret societies exist. The big ones aren't even so secret any more, like the masons. I've seen people that have masons bumper stickers. You google search and find free mason lodges, such as http://www.scgrandlodgeafm.org/. I don't believe them to be all that insidious, either. Just kind of a rather exclusive club that just happens to be in a lot of places and might have a little bit of influence.