I have an idea for an app that would be used for the government and when I say it can be used for the government I mean that I can't just make it and people can use it. The app would have to be government protected and stuff. Is there a website or something that I can go on to patent this app idea?
Your best bet for a situation like this is to speak with a patent professional in your area. Patents aren't something to be taken lightly--they're typically an expensive and time-consuming venture.
Your instinct to avoid disclosure is reasonable, just to protect patentability. It'd be best to speak with a professional to whom you can disclose your invention and discuss what aspects of your app might be protectable.
Patent applications that the USPTO feels may pose a threat to national security are reviewed on a per-case basis, and if appropriate, they'll keep it secret. There's a review process that I can go find details on if you'd like, but the first step either way would be to speak with a patent attorney or agent.
Even if you find a website for this, it's very likely a scam (and they're definitely out there). So do be careful if you find one.