The city of Geneva, represented by lawyer and former French Minister for the Environment Corinne Lepage, filed the complaint on March 2nd, according to Le Temps, arguing that the plant endangers people's lives and causes water pollution.
Geneva is located close to Swiss border with France and the plant is located roughly 70km from the city.
In March of last year, Geneva announced its intention to take a firmer line with the reactor, and now judges will investigate the complaint.
The Bugey nuclear site creates about 4.5 percent of France's electricity and is one of the oldest in France.
Situated in Saint-Vulbas in Ain, the site is 100 hectares and employs 1,200 people. It generates electricity using pressurized water reactors, using cooling water from the nearby Rhône River.
It has been the subject of controversy before, notably in 2013 when Greenpeace activists broke in to the plant to highlight alleged security weaknesses at the facility.
In July 2015, French lawmakers adopted a new law that will see the country's energy consumption halved by 2050 as France attempts to slash its reliance on nuclear energy.
France has been forced to step up security at its nuclear plants fearing that terrorists may try to target them.
"We are working with police and the gendarmerie to carry out systematic checks of everyone entering nuclear power stations,” Jean-Bernard Levy, president of French state power company EDF told France 2 television.