The station was sealed off while police detained a man with a replica gun which fires blanks, the local prefecture told the AFP news agency.
Spanish media reported earlier that shots had been fired and social media users bombarded Twitter with worried messages, but the prefecture denied there had been any violence.
"No shootout at Nimes station," it said, describing it as an "operation to check a suspicious sighting," and rail traffic was expected to resume shortly.
The incident coincided with the start of the Vuelta a Espana, one of Europe's leading cycling races, which this year kicks off just outside Nimes.
A heavy police presence was deployed for the event, which took place less than two days after terror attacks in the northeastern Spanish province of Catalonia that killed 14 people and injured 120.