President Juvenal Habyarimana's plane was hit by a missile as he flew into Kigali.
His death triggered the genocide that left up to one million people dead.
France has issued international arrest warrants for nine of Kagame's associates over the killing.
Up to 25,000 demonstrators, including survivors of the genocide, gathered in the capital's Amahoro stadium on Thursday singing anti-French songs and burning French flags.
Some protesters carried signs that said, "France: Stop Organising a Second Genocide."
The arrest warrants were issued on Wednesday by Jean-Louis Bruguiere, a French anti-terrorism judge.
|"The final order to attack the presidential plane was given by Paul Kagame himself during a meeting held in Mulindi on March 31, 1994" |
Arrest warrant request by Jean-Louis Bruguiere, French anti-terrorism judge
Bruguiere says that Kagame instructed his Rwanda Patriotic Front (RPF) to shoot down the plane.
"The investigations undertaken have clearly shown that for the RPF, the physical elimination of President Juvenal Habyarimana was the necessary pre-condition for seizing power by force, and was inscribed in a vast plan worked out to this end," Bruguiere wrote in the warrant request.
"The final order to attack the presidential plane was given by Paul Kagame himself during a meeting held in Mulindi on March 31, 1994," the document said.
The killing of Rwanda's president, a Hutu, sparked massacres of Tutsis and moderate Hutus in the central African nation.
About 500,000 people, mostly ethnic Tutsis, were killed by extremists members of the Hutu majority in 100 days.
Kagame reacted to the decision by calling the judge "an impostor, a politician" in an interview with France-Culture radio.
"There is no doubt" that ties between France and Rwanda will suffer, he said.
He also told the BBC that the arrests warrant were "not really a judicial process as such, it's a political process".
Relations between France and Rwanda have been strained for years. Kagame has previously accused France of doing too little to stop the genocide.
Under French law the warrants mean the suspects have been placed under official investigation and could now face questioning by the French judge.
A warrant cannot be issued for Kagame because he enjoys diplomatic immunity as a serving head of state, but a judicial source said Bruguiere had written to Kofi Annan, the UN general secretary, asking for Kagame to be brought before the International Criminal Tribunal for Rwanda.
The French court is able to investigate the case because the crew of Habyarimana's plane was French. The families of the pilot, co-pilot and mechanic, who all died in the crash, filed a suit in France in 1998.