Sosthene Munyemana, 45, who had been working in a hospital in Bordeaux for eight years, denies the charges.
His arrest on an extradition warrant from Rwanda comes weeks after France and Rwanda restored diplomatic ties.
France had rejected an asylum bid by him in 2008, saying there were "serious reasons" to suspect his involvement in war crimes in 1994, AFP reported. Some 800,000 Tutsis and moderate Hutus were killed in the 100-day massacre in 1994.
Mr Munyemana was released on bail, but must report to judicial officials until a court date is set.
He had been on the Interpol list of wanted men for a few years.
The arrest comes weeks after French Foreign Minister Bernard Kouchner made his first visit to Rwanda since diplomatic ties were restored in November. Relations between Paris and Kigali had been poor for several years but were severed in 2006 after a French judge accused President Paul Kagame and several senior officials of being behind the 1994 murder of Rwanda's Hutu President Juvenal Habyaremana.
The shooting down of his plane triggered the 1994 genocide.
Those suspected of being most responsible for the killings are being tried by the International Criminal Tribunal for Rwanda (ICTR) based in Arusha, Tanzania.
