When a little green man from Mars approaches you and says, "Take me to your leader," who are you going to call? "Your leader" could be anyone from your father to the mayor to the president, but getting any of those people to take your call is another thing entirely. Calling 911 might even get you arrested when you tell them what your emergency is. Do we even have a protocol for alien contact? Gizmodo called around to various authorities to find out, and mostly found out how they all passed the buck on such calls.
Bertram Kelly, Public Affairs Team Lead, Centers for Disease Control
UFOs are not in the scope of research work performed by the CDC. We suggest you reach out to NASA for any information regarding UFOs.
Catharine “Cassie” Conley, Former Planetary Protection Officer, currently a researcher at NASA
That would depend if it’s a big alien or a little alien. If it’s an intelligent alien, that’s actually probably [the responsibility] of the Air Force, other militaries and probably the UN. If it’s a tiny alien, you wouldn’t know you ran into it.
Daryl Mayer, 88th Air Base Wing Public Affairs
To be honest, we don’t have any guidance here about such an event. You might be able to get more from the Pentagon Press Desk, but I’m not sure.
There are plenty more opinions and procedures from everyone from the NYPD to the Astronomy Department at Harvard, at Gizmodo.