Franco-Rwandan Claude Muhayimana was arrested and charged in Rouen overnight Wednesday as part of a French inquiry into the genocide.
According to a lawyer representing the Rwandan government, he took part in a massacre of several thousand Tutsis at a church in Kibuye, western Rwanda, and another in a stadium where 1,000 were killed the following day.
In February a top French court ruled that Muhayimana, who has had French nationality since 2010 and works for the Rouen city council, could not be extradited because Rwanda's application was based on laws passed after the alleged crime took place.
On Thursday a court in Aix-en-Provence turned down another extradition request on the basis of that decision.
Muhayimana was rearreted after a genocide survivors' group, the CPCR, brought a new case aginst him and it has taken the same action against Pierre Tegara, the subject of Thursday's judgement.
Following Kagame's repetition of charges of complicity last weekend, Le Drian addressed a morale-boosting message to the troops on Thursday, defending the "honour" of France's military.
Saying that "some accusations cannot be left unanswered", he said that it was to the "honour of France and its armed services to have, before anyone else, reacted to the tragedy that was unfolding before the eyes of a paralysed international community".
In his first speech to parliament as prime minister on Tuesday, Manuel Valls called Kagame's accusations "unjust".