Well there is the case of Kurt Sonnenfeld who was the official FEMA videographer at ground Zero. He has fled to Argentina and published a book about the whole issue: http://www.voltairenet.org/article160666.html

As a historical example you have Israel's nuclear program and there was exactly one whistle blower, Mordechai Vanunu and he was hunted down and thrown into prison for that. So imagine the amount of people involved in a nuclear program and yet you find only one who speaks out. The thing is, people who are in the know also know why they have to keep quiet and the consequences they will face if they do otherwise.

Lets imagine that some hypothetical government agent starts speaking, how could he prove his point? And even if he could wouldn't that speak against him because if he was involved why didn't he say so earlier or do something against it? He probably would be dismissed as another lunatic.

EDIT: There is also the ringworm affair that happened in the 40s and 50s in Israel and is still controversial and a lot of people have kept quiet about it for decades.