The court on Wednesday overturned a November appeals court ruling that Claude Muhayimana and Innocent Musabyimana could be extradited and upheld a September decision by a court in Douai, northern France, that Laurent Serubuga could not.
Genocide was made a punishable crime in Rwanda after laws were passed in 1996 and 2004.
Muhayimana, who obtained French citizenship in 2010, is accused of taking part in the mass murder of Tutsis in the western town of Kibuye, while Musabyimana is accused of genocide in the north-western province of Gisenyi.
Serubuga, who a deputy chief of staff of the Rwandan army at the time, was detained in France last July because of an arrest warrant issued by a Rwandan court.
The Douai court rejeved the extradition call on the grounds that the warrant was issued 10 years after the alleged crimes.
France has been reluctant to extradite Rwandans and its relations with Kigali have been tense since President Paul Kagame came to power 20 years ago.
Muhayimana could be tried under the same laws and an investigation into his possible involvement in crimes against humanity was opened last June.
The leader of the Rwandan genocide survivors' association Ibuka, Jean-Pierre Dusingizemungu, slammed Wednesday's decision, saying Rwanda had a "proven"
system in place to try genocide suspects.
"France is not really making any effort," he said. "Our view is that France is hesitating because it is involved. Perhaps it wants to protect its old friends."