This story was one of several published together that I read in paperback form sometime in the mid-1990s. It takes place in a period after the collapse of an interstellar human empire, and it follows a man who is part of a new and rising empire that is re-establishing contact with "lost" worlds.
The function of this man's service bureau is to identify which planets might be dangerous to the new empire. His job is to spend time on newly-contacted planets to evaluate their culture for signs of militaristic and/or aggressive tendencies. If these tendencies are found, he is to notify a separate service that will come in and (I think) place the planet under martial law, then take whatever steps are necessary to neutralize the threat.
In this story, the man is nearing the end of his evaluation period, and, even though he hasn't found anything that constitutes good evidence of a threat, he is deeply uneasy about giving the all-clear signal. He eventually decides to risk bureaucratic backlash by sending the danger signal, and a secondary inspector from the other service arrives.
The new arrival quickly confirms his concerns, saying that it's one of the "worst cases" he's seen. He is able to point out the various features that constitute proof positive that the natives are actively hiding their true nature. One of these features is that all of the roads are along high points in the geography, i.e. not dipping in and out of valleys or depressions but following ridges that allow clearer views of the surrounding area. I think another feature involves their vehicles, which have design features better suited to military use, though I'm less certain of this.
The new arrival congratulates the protagonist on his insight and invites him to become an agent of his own service, which the protagonist accepts. The other stories in the book follow the same protagonist through his subsequent adventures.
I want to say that the author was one of the bigger names in science-fiction at that time, but trawling through various bibliographies hasn't turned up anything that looks promising. I have in particular looked over the works of Keith Laumer (e.g. Retief series), as it reminded me of the same style, though less humorous. I don't believe that this is a Laumer work, but I could be wrong.
Note that I'm tagging this as "novel," because I remember it as being a somewhat separated story, but not with its own title -- more like a vignette within a single book. All of the vignettes were about the same person.