Someone who's described as being low-level has very little authority in their job or position. A low-level employee at the F.B.I. might be the person who answers the phone, or who cleans people's offices at the end of the day.
A low-level police officer's job might involve giving speeding tickets, rather than investigating murders, and a low-level librarian might be stuck shelving books, instead of ordering new ones or archiving historical manuscripts. Another meaning of low-level is physically low, or at a low altitude: "I feel like I could almost touch that low-level cloud."