The AP news agency said Munyemana had been freed under judicial control after his arrest, meaning he must report to judicial officials until his appearance before a court that will decide his fate.
A French court rejected the doctor's asylum request in 2008, ruling that there were "serious reasons" to suspect he was involved in crimes against humanity, a decision which Munyemana has since appealed.
His arrest comes weeks after Bernard Kouchner, the French foreign minister, travelled to Kigali, Rwanda's capital, in the first high-level visit since Paris France and Rwanda agreed in November to resume diplomatic ties.
Rwanda broke ties with Paris in 2006 after a French judge issued warrants for nine officials close to Paul Kagame, the president, who were suspected of being implicated in the shooting down of the plane of a former Rwandan president.
That incident is considered to have triggered the start of the genocide, which saw the massacre of mostly ethnic Tutsis carried out by the majority Hutus.