As Rwanda marked the genocide's 10th anniversary, a French minister cut short his trip after strong criticism from the country's president.
Rwandan Tutsis in Paris commemorated the genocide
At a ceremony in the capital, Kigali, Paul Kagame repeated accusations France had trained and armed the Hutu militias who carried out the mass killings.
But he acknowledged the Rwandan people themselves bore primary responsibility.
The French Foreign Ministry rejected the accusations and described them as "running counter to the truth".
A spokeswoman confirmed that French junior foreign minister Renaud Muselier had decided to cut short his trip to Rwanda over the matter.
Mr Kagame's accusations come after a French police report - leaked to the daily Le Monde - concluded he gave direct orders for the rocket attack on then President Juvenal Habyarimana's plane.
The death of President Habyarimana, a Hutu, triggered the 1994 genocide in Rwanda in which some 800,000 people died, most of them Tutsis.
1994: RWANDA'S GENOCIDE
6 April: Rwandan Hutu President Habyarimana killed when plane shot down
April -July: An estimated 800,000 Tutsis and moderate Hutus killed
July: Tutsi-led rebel movement RPF captures Rwanda's capital Kigali
July: Two million Hutus flee to Zaire, now the DRC
Tens of thousands of people attended Wednesday's ceremony in Kigali, including many survivors of the genocide, who were overcome with emotion.
Earlier, a national memorial was unveiled to the dead, on a hilltop overlooking the capital.
Ceremonies were also held at the United Nations in New York and in Rome.
The recent dispute between the two countries is nothing new.
Correspondents say relations between France and Rwanda have long been tense over France's alleged role in the genocide.
France became close to President Habyarimana's government shortly after independence and replaced the ex-colonial power, Belgium, as Rwanda's main western backer.
When the Tutsi-dominated rebel army, the Rwandan Patriotic Front (RPF), first launched its war against the Hutu authorities in the early 1990s, France sent soldiers to Kigali.
The French helped stop the RPF advance and then stayed on, officially as military advisors right up to the start of the genocide.
The BBC's world affairs correspondent Mark Doyle says it is no secret that the French had officers attached to train and arm Rwandan military units which subsequently committed genocide.
France vehemently denies any direct involvement in the mass killings.