"They are the same ones who are still killing in the DRC. The macabre stories from Kipupu are in a straight line from the massacres that have hit the DRC since 1996," the 2018 peace prize winner said in a tweet.
Civilians in Kipupu, a village in South Kivu on the Fizi heights overlooking Lake Tanganyika, came under attack on July 16, with the death toll ranging widely between 18 and 220.
Kivu Security Tracker (KST) researchers gave a death toll of 18 based on a network of local sources, while provincial lawmakers released a statement saying 220 people were killed.
The UN peacekeeping force known by its French acronym MONUSCO has launched a probe into the massacre, blamed by all sources on a coalition of three Banyamulenge militias.
It noted that neither MONUSCO nor the Congolese army were present in the area of the massacre. Soldiers have since been deployed to the village, the army said Thursday.
The area has seen violence between the Banyamulenge community -- the descendants of ethnic Tutsi migrants who came from Rwanda -- and other local communities such as the Babembe for the past year.
Social media and a citizens' group, Filimbi, levelled harsh criticism at MONUSCO and the central government of the vast central African country.
"What justifies this silence and this indifference on the part of everyone -- the national authorities (and) MONUSCO?" Filimbi said.
On Saturday, a readout of a cabinet meeting the day before made no mention of the Kipupu killings.
KST is a joint project of the Congo Research Group, based at New York University’s Center on International Cooperation, and Human Rights Watch.
Mukwege, a gynaecologist from South Kivu, was awarded the Nobel Peace Prize for his work treating women victims of sexual violence.
Dozens of armed groups exert a bloody grip over the provinces of North and South Kivu and Ituri, largely as a legacy of the region's two wars of the 1990s.