Sosthene Munyemana, 45, who had been working in a hospital in Bordeaux for eight years, denies the charges against him.
His arrest on an extradition warrant from Rwanda comes two months after France and Rwanda restored diplomatic ties.
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France had rejected an asylum bid by him in 2008, saying there were "serious reasons" to question his involvement in war crimes in 1994.
But he was arrested and detained by French police at the end of January following an extradition warrant issued by Kigali.
Dr Munyemana is understood to have been on an Interpol wanted list since 2006 and Rwanda had been seeking his return for more than a decade but until recently the French authorities had delayed proceedings.
Dr Munyemana who previously worked as a gynaecologist at the University Hospital in Butare, is alleged to have been involved in the massacre of 800,000 Tutsis and moderate Hutus in the 100-day massacre in 1994.
He has been referred to as the "butcher of Tumba" but Dr Munyemana himself says he is the victim of false accusations.
Campaigners for justice for the Rwandans killed in 1994 have welcomed Paris' change of heart after years of hostile relations between the two governments.
Dr Munyemana has now been released on bail, but must report to judicial officials until a court date is set.
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 Habyarimana.
The shooting down of his plane triggered the 1994 genocide.
Rwanda has in turn accused France of being partly responsible for the 1994 genocide because its armed forces had backed the Hutu regime of President Habyarimana.
A government appointed panel in Rwanda found last autumn that Hutu extremists in the 1994 government were responsible for Mr Habyarimana's death and that France was not involved.
Since the end of last year the thaw in relations between the two countries has even led Mr Kouchner to say that in future France and Rwanda should "work together so our countries know what has happened."
Those suspected of being most responsible for the killings are being tried by the International Criminal Tribunal for Rwanda based in Arusha, Tanzania.