The meeting follows a recent meeting between the Rwandan and French presidents in Lisbon, Portugal, during the European Union Summit.
Kouchner stated, in the presence of Kagame, that "the legal, historic and the political problems needed to be separated.
President Kagame said he wants to get rid of the obstacles based on the errors of the past" to be able "to move forward".
Mr. Kouchner held discussions with the Rwandan president for about an hour before holding a press conference where he evoked a "political fault" by France.
According to Rwandan radio, a delegation from Kigali would travel shortly to France.
The French top diplomat also visited the genocide memorial centre where he laid a wreath of flowers.
The diplomatic relations between Paris and Kigali have been interrupted, on the Initiative of Kigali, since November 2006 when the French Judge Jean Louis Bruguiere issued nine arrest warrants against acquaintances of President Kagame accusing them of being the organizers of the attack against the plane of President Habyarimana.
He had also wanted that President Kagame to appear before an International tribunal.
Last week, in a tribune published by the French newspaper Le Figaro, the head of the French diplomacy wrote that "France and its soldiers in no way incited, encouraged, helped or supported those who orchestrated the genocide and who started it in the days which followed the attack (...) our rapprochement with Rwanda will not be made at the detriment of the honour of the French Army nor of historical truth".
PB/MM/SC
© Hirondelle News Agency