This mysterious guy has one menacing line in the whole movie. As Corman and Lucas assign Willard his mission to kill Kurtz, the civilian makes the nature of that mission totally clear, telling Willard:
CIVILIAN: Terminate with extreme prejudice.
We don't actually know who he is, but he's apparently some important government person, concerned about what Kurtz is doing and how it will reflect on the higher-ups. Actually, we do know who he is. In addition to his bit acting part, Jerry Ziesmer was the assistant director on the film.