On 18 October 1995, four French and Rwandan citizens living in France, supported by three non-governmental organizations (the Collectif girondin pour le Rwanda, Survie and the International Federation for Human Rights, known as FIDH), filed a complaint against Munyemana in Bordeaux containing allegations of genocide, torture and other cruel, inhuman or degrading treatment, and asked for his arrest. They also decided to become civil parties to the subsequent proceedings. In 2001 the investigation was transferred to Paris.
In 2006 Rwanda issued an arrest warrant against Munyemana on charges of “participation in war crimes and genocide”.
In January 2008 the French National Court for Asylum dismissed the asylum application of Munyemana. The French Office for the Protection of Refugees and Stateless persons (OFPRA) stated that the application was not sincere and aimed at hiding a truth. Furthermore, there were reasonable grounds for considering that the applicant had committed genocide and crimes against humanity. Therefore, pursuant to Art 1(F)(a) of the 1951 Geneva Convention on the Status of Refugee, he was excluded from such protection.
In October 2008, Munyemana was convicted in absentia by the Butare’s Gacaca, traditional Rwandan Courts. He was sentenced to life imprisonment for his crimes committed at the Butare hospital and to 30 years of imprisonment for the crimes committed in Tumba.
On 20 January 2010, he was arrested by the police in Bordeaux on the basis of the previous arrest warrant issued by Rwanda, which also asked for his extradition. Subsequently he was released on probation, waiting for his initial appearance in front of the Court of Appeal. On 19 October 2010, the Bordeaux Court of Appeal dismissed the Rwandan request for extradition on grounds of inaccuracy of the request. The Court also lifted the probation against Munyemana.
On 30 January 2011, the Collectif girondin pour le Rwanda organized a demonstration in front of the hospital where Munyemana works in France. Munyemana filed a complaint against the Collectif and on 8 November 2011, the Collectif was convicted by the Tribunal of Bordeaux for breach of presumption of innocence.
On 14 December 2011, Munyemana was indicted in Paris for genocide and crimes against humanity and put again under judicial control. On 9 May 2017, the investigating judge within the Paris Tribunal informed the parties that he had completed his investigation.
On 11 May 2018, the prosecutor of the French war crimes unit issued his final submission.
On 13 June 2018, the International Federation for Human Rights (FIDH), together with the League of Human Rights (LDH) and the Collective of Civil Parties for Rwanda (CPCR) in their concluding observations demanded that Sosthenes Munyemana is brought to justice.
On 3 December 2018, the investigating judges referred the case to the competent criminal court.