Most large US companies if they want to have the government as a client, have special rooms with employees with security clearances that work mostly on projects that the CEO and even their line managers do not know what they are. HR also have a special employees or a private section that deal with these people. There is some deniability also: the managers can tell the truth under oath and say they have no knowledge about the projects!

It's part of normal business operations not some secret illegal shady kick backs operation within some kind of spy movie.

There's no need to secretly infiltrate a company when the company is working happily with you. People underestimate how close big business and 3 letter agencies actually are in many cases.