Whistle blowers are prosecuted vigorously and do not get the benefit of the doubt.
When dealing with a government entity you should probably do nothing, as the risks outweigh the rewards at this time. If you still feel like speaking up, raise the issue with your boss in one email, carefully and politely, and file a hard copy of the email somewhere safe. Do not go up the food chain, do not go to the press. If there is a crap storm the hard copy may save you, but even that is not assured.
The default position should be to protect yourself and your family, and not stick your neck out. We have too many examples that show that even the best intentions may result in the messenger being vigorously prosecuted.