The African weekly Jeune Afrique quoted Kagame last month as saying in an interview that both France and Belgium had played a "direct role ... in the political preparation of genocide and participation in its execution".
The French Foreign Ministry said France was "surprised by the recent accusations made by the Rwandan president", and that French Justice Minister Christiane Taubira, who had been due to travel to the Rwandan capital Kigali on Monday, would no longer attend the commemoration.
"These accusations are in contradiction with the process of dialogue and reconciliation that has gone on for several years between our two countries," the ministry's statement said.
The armed forces of Kagame's Rwandan Patriotic Front defeated government troops in 1994, stopping a three-month wave of bloodletting by ethnic Hutu extremists in which more than 800,000 minority Tutsis and politically moderate Hutus were killed.
Before the genocide, France was Rwanda's main Western backer. But in its aftermath, their relations collapsed as Kagame accused France of training and arming the Hutu militias who were the main force behind the slaughter - an accusation Paris always denied.
Latterly he had appeared to drop the issue, however, as France acknowledged mistakes and created a genocide investigation unit as the two countries began to rebuild their relationship.
Last month, a Paris court sentenced a former Rwandan soldier to 25 years in jail for his role in the genocide in the first such trial to be held in France.