MJ12 does not operate in a vacuum, as a standalone, off-the-books, agency. It has tentacles whereby it reaches out to gather information and accomplish its goals. MJ12 is the administrative hub, where policy decisions are reached and the center where key contacts with the outside world are maintained. However, it would be short-sighted indeed, in that those in its hierarchy have parallel positions within the federal bureaucracy, to not use those very bureaucracies. In fact, given the structure of MJ12, it is only natural. Without being specific, we will enumerate some of those tentacles.
Should the reader find this astonishing - that federal employees are regularly dealing with MJ12 yet the public hears at most rumors of this activity - they should bear in mind the following. Intelligence groups, and the military in general, operate on a need to know basis. This rule is in place to prevent covert operations from being carelessly exposed, the enemy from learning of plans, and to a small degree to prevent the public from learning what the government is really up to. Also, when services are performed for MJ12, these services are not distinguishable from normal, everyday services. The requests don't have MJ12 stamped in big bright letters on the front, they come wrapped in commonplace covers, and thus raise little suspicion.