Fighters from the National Congress for the Defence of the People (NCDP) of Laurent Nkunda, who says he is fighting to protect ethnic Tutsis, then won control of the village and killed those who they thought supported the Mai Mai.
The UN mission said on Friday its investigators had "visited 11 communal grave sites, containing at least 26 bodies, fighters and civilians".
Anneke Van Woudenberg, a researcher with Human Rights Watch, and Colonel Jean-Paul Dietrich, a UN military spokesman said it appeared the rebels had committed many more executions than the militia.
Some residents told the Associated Press news agency that many victims were shot in the head, while other said the rebels dressed the dead in military uniforms.
The killings highlighted the inability of UN peacekeeping forces to protect civilians across the huge region.
The UN mission in DR Congo (Monuc) has a base in Kiwanja, but it only has 120 soldiers to protect up to 50,000 people.
"Sadly we can't protect every person in the Kivus [provinces]," Doss said.
Al Jazeera's Mohammed Adow, reporting from Goma, said that the peacekeepers had managed very little success.
"The UN is there and has been sending teams to the battle scenes. But they can only stand around and watch as the fighting continues," he said.
"In Goma, the UN has only 850 personnel ... They are outnumbered - there are thousands of rebels and thousands of government forces."
Dietrich said that UN forces had been pinned down under crossfire for some of the first day of the killings and were hampered because militiamen were hiding in houses among civilians.
Peacekeepers were also trying to stop NCDP attacks on two other towns, Nyanzale and Kikuku, while the killings continued on Wednesday .
"It's very difficult to protect thousands of civilians, especially at night,'' Dietrich said.
Meanwhile, thousands of people were on the move again as they flocked towards overcrowded refugee camps amid a relative lull in days of fighting between government forces and the rebels.
"There is little available to take care of [people displaced by the fighting]," Adow said. "They are going to camps that are already overcrowded, and as the fighting nears the camps they are displaced once again.
"Some people are sleeping on the side of the road; there is little aid getting to them.
The UN estimates that about 253,000 people have been displaced since September.