"Everyone is scared of genocide today after what happened in Nazi Germany. Everyone is scared of chemical weapons and I think we have drawn a red line... but when it comes to using rape as a weapon of war we equivocate," Mukwege told AFP in Sweden.
Mukwege, who is in Stockholm to receive a prize from the Right Livelihood Foundation, has set up a hospital and foundation to treat rape victims, and has for several years been considered a favourite to win the Nobel Peace Prize.
Women are frequent targets in conflict-torn eastern DR Congo, and the doctor recounted harrowing stories of women who have been raped in public in front of their husbands and children and arrive at the clinic with their genitals burnt and tortured.
Mukwege said rape as a weapon of war had dramatic consequences for women and for the country.
"It destroys women and society, it produces children without filiation... women who can no longer give birth. This constitutes a genocide because when you destroy the female genital organs you diminish her and prevent population growth," he said.
Every year, his hospital's main programme for victims of sexual violence takes in more than 3,500 women and provides them with reconstructive surgery.
"The inability of DR Congo to sort out its problems followed by the silence of the international community is a major drama of our time," the doctor said.
"We are in the 20th year of atrocities and I think that the more the years go by the more we see the groups, the militias improve their tool of torture," he said.
Mukwege pointed to a United Nations resolution adopted in 2000 as an example of good intentions. "But there is not a solid red line yet which says: this limit can not be passed," he said.
UN resolution 1325 calls on all member states to take specific measures to protect women and young girls, especially against rape.
Mukwege's work has earned him numerous nominations for the Nobel Peace Prize, and he has also been honoured with an award from the UN for his human rights activities.
Last October Mukwege narrowly escaped being murdered after a group of armed men broke into his home in Bukavu. He was forced into exile in Belgium and returned to his hospital in January this year.