Three days of national mourning have been declared following Saturday night's mass killing, the latest in a series of massacres that have left more than 600 people dead in and around the troubled town of Beni since 2014.
Speaking to a local radio station, Beni mayor Edmond Masumbuko said 42 people had been killed. The government had earlier put the death toll at 36.
Army spokesman Mak Hazukay said the attack was carried out by the Allied Democratic Forces (ADF), a partly Islamist armed group of Ugandan origin.
Hazukay said the ADF rebels had "bypassed" army positions "to come and massacre the population in revenge" for military operations in the area.
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The victims were found in Rwangoma, a neighbourhood on the outskirts of Beni, according to government spokesman Lambert Mende.
Mende said the government has previously sought to "alert the world to the jihadist threat" in DR Congo, adding: "In our country, the armed forces of the DRC are alone in the face of the indifference of the international community".
Local human rights activist Jackson Kasereka said residents in north Beni were burning tyres in the streets.
"The police have just taken the body off us but we will continue to protest. It's not normal that they slaughter us like goats," said motorcycle taxi driver Georges Kamate.
"Our government is incapable of keeping us safe!" shouted another protester.
The killings came three days after Kabila visited the region, promising to do everything in his power to bring peace and security.
"There is a blatant lack of security, (the authorities) are not capable of keeping the population safe. That is why these people have come into the street," he said.
Government spokesman Lambert Mende announced three days of national mourning would begin from today.
"Flags will be lowered to half-mast across the country and media scheduling will be adjusted to the situation," he said.