According to the French prefecture where Nimes is located, a return to normal operations is "imminent".
Earlier it was reported that men had "jumped off the train and started shooting" - but that has been denied by police this evening.
Another security official said police are working to verify whether the incident had any link to the attacks Thursday around Barcelona. However, local authorities have now released information saying that no shots were fired, but that there was a possibility that armed men were on board a train.
A national police spokesman said the operation began when a passenger alerted police to a man with a weapon.
Local police have advised people to steer clear of the area surrounding the train station where gunshots were reportedly heard and which has been evacuated.
French authorities increased checks of its border with Spain after the attacks, and one suspect is believed at large.