Kagame is displeased at the reopening of the investigation into the 1994 assassination of Habyarimana Juvenal
"The judicial system of Rwanda is not subordinate to France or France's interests," Kagame told a cheering audience of judges, senior military officers and government officials at an official judicial function.
"It should be France in the dock being tried, not anybody in Rwanda and not Rwandans."
Rwanda's former chief of army staff Faustin Kayumba Nyamwasa, now in exile, has accused Kagame of being linked to the shooting down of the plane carrying president Habyarimana Juvenal, the president of Burundi and a French air crew.
Nyamwasa made the accusations against Kagame in a widely reported trial in 2012, two years after an attempt to murder Nyamwasa in South Africa.
Kagame says the plane was shot down by Juvenal's own supporters who disapproved of a peace deal Juvenal had negotiated with Kagame's rebels.
The shooting down of the plane unleashed a slaughter in which ethnic Hutu extremists killed more than 800,000 Tutsis and moderate Hutus.
The investigation was opened in March 1998 after a complaint by the families of the French crew of the plane. It has been closed twice because of problems evaluating the evidence but was reopened after Nyamwasa requested to be heard by investigators.
The French judge in charge of the investigation has asked South Africa, where Nyamwasa lives, to be given permission to question him, according to a French judicial source.
French judges have previously called for senior Rwandan military officers, including Kagame, to be put on trial for shooting down the plane.
Before the genocide, France was Rwanda's main Western backer. But their relations collapsed after the genocide as Kagame accused France of training and arming the Hutu militias who were the main force behind the slaughter - an accusation Paris always denied.