I think it's still unlikely. In the case of the Manhattan project, the USA government wasn't racing against private companies but against other governments. Therefore, all advances in the field where highly secret. In this case, the CIA would be racing against private companies as well, which are hiring the best physicists and engineers too. So, while it's possible that a governmental agency is ahead of what it is publicly know, I doubt that they would be dramatically ahead. This is similar to part of the argument I would present if someone asks me why I believe cryptography in general is secure.