"You can accused France of a lot when it comes to political errors that have been made, on they way things happened ... but 'direct participation'? I don't think so," Kouchner, who as foreign minister under President Nicolas Sarkozy started a thaw in relations between the two countries, said when interviewed by RFI in Kigali.
In an interview published ahead of the commemoration, Kagame renewed longstanding accusations that French forces played an active role in the slaughter that preceded his Rwandan Patriotic Front coming to power.
France responded by calling off Justice Minister Christiane Taubira's participation in the ceremonies.
On Sunday Rwanda's Foreign Affairs Minister Mushikiwabo declared it "impossible for our two countries to move forward if the condition is that Rwanda has to forget its history in order to get along with France".
"For our two countries to really start getting along, we will have to face the truth, the truth is difficult, the truth of being close to anybody who is associated with genocide understandably is a very difficult truth to accept," she told reporters.
The French boycott was an "overreaction", she said.
"I don't think the French people in general should be held in ignorance of what some French officials did in this country," she added. "Specific individuals in the military and the politics did some very wrong things in this country."