No details were ever given in the show, but the implication was that Gus was part of the Pinochet government in Chile. See for confirmation this interview with the actor who played Gus:
which includes this:
Gus was probably a guy who was a General at some point or a Lieutenant and had probably killed a lot of people — or maybe was a hero in the army.
That's about as official as it gets for this question.There's a ton of fan speculation based on the few tiny clues that made it into the show (google "Gus Fring Pinochet" to see some of it).
Another interview, this one with Vince Gilligan:
in which he says that the vagueness is intentional:
It has something to do with the Pinochet government, we think, but that’s about as close as we’ve gotten. At the end of the day, try not to nail down anything that we don’t have to.
I enjoy it when I’m given by the creator of a show or a movie all the elements that will keep me interested in the story, but leave a few aside so I can do a little of the work myself.
Both of those interviews are from around the end of the 4th season (when Gus was killed) and there was the possibility that we might still learn more of Gus's backstory through additional flashbacks, but that never happened so the nonspecific "associate of Pinochet" is all we have.