The witness, who has been questioned twice but has not been named, says he helped load two surface-to-air missiles at the headquarters of Kagame's Rwanda Patriotic Front (RPF) to be taken to Kigali, where they were allegedly used to take down Habyarimana's plane.
He also says that two men, Franck Nziza and Eric Hakizimana, later told him they had fired the missiles.
The French judiciary, which is acting on a legal complaint from French citizens killed aboard Habyarimana's plane, decided in October 2016 to reopen its investigation into the assassination.
Defence minister charged in France
So far a total of seven people have been charged in France over the deaths, including Rwanda's current Defence Minister James Kabarebe.
The witness says that he was part of Kabarebe's bodyguard at the time and that Kabarabe boasted about the success of a mission on the date of the killing.
Investigating magistrate Clément Herbo has ordered a confrontation between the witness and Kabarebe and Nziza in December.
The man claims to have taken refuge in Uganda after being ordered to eliminate a colleague working in the missiles section of the RPF's headquarters.
The Rwandan government has rejected all accusations of RPF involvement, claiming that the missile was fired by a hardline Hutu faction in the army of the time
.A Rwandan investigation has accused 22 French army officers of involvement in the genocide.