Theron suffered the unspecified injury while doing her own stunts in a wire-hanging action sequence, the movie's publicist, Jeanmarie Carrasco, told The Associated Press Tuesday.
"No cuts, no broken bones," Carrasco said. "I think it was something less tangible than that. ... Something vague and nagging."
No one else was hurt, Carrasco added.
Filming in Berlin has been halted for several weeks to allow Theron to recover. It wasn't known if the injury would require script changes or when the movie would resume production.
Theron's publicist said the 29-year-old actress wasn't hospitalized.
"She did sustain an injury on the set. It's a very physically demanding role," said Theron publicist Amanda Silverman.
"Aeon Flux" is set centuries in the future at a time when a plague has wiped out most of the population. Theron plays the title character, a sleek, sexy commando who is part of a rebellion against the remaining government.
The "Aeon Flux" story was once depicted in a series of animated shorts on MTV.
Theron, who won a best actress Oscar for her role in "Monster," stars in the film "Head in the Clouds," set for release Sept. 17. In it, she plays a French socialite living it up on the eve of World War II.