An estimated 800,000 people - mainly members of Rwanda's Tutsi minority - were killed during the genocide two decades ago.
Many of the victims were hacked to death. Their number included ten Belgian paratroopers, who were serving with the UN in Rwanda.
Mr Di Rupo said that the victims had paid a high price for their dedication and generosity: "This ceremony of remembrance is a way of saying 'never again'".
Guy Verhofstadt, the Belgian premier at the time, and his foreign minister, Louis Michel, also attended the ceremony.
Afterwards relatives of the murdered Belgian paratroopers and an official Belgian delegation headed by foreign minister Didier Reynders flew out to Rwanda to attend Monday's official ceremony of remembrance.
On Saturday the Rwandan President, Paul Kagame, attacked both France and Belgium saying that France took part in the genocide and that Belgium was involved in the political preparation of it. As a result France pulled out of the commemoration ceremony. Belgian foreign minister Didier Reynders indicated that Belgium was not following suit.
"I understand the French reaction. As far as Belgium is concerned, we have heard this reaction (from Rwanda) so many times already. (Belgium's parliamentary) commission of enquiry provided a very clear answer. Now we are going to continue with a commemoration of the victims and their family. We are not paying tribute to the president or his government."
On Monday Belgian Premier Di Rupo and defence minister De Crem are also attending a ceremony at the Tomb of the Unknown Warrior in Brussels to commemorate Belgian victims who fell during UN peace missions.