The violence is focused in North Kivu near the border with Rwanda where warring groups have targeted villages seen as supporting their opponents, while the national army has been diverted to fight a movement of mutineers known as M23.
"The deterioration of the overall security situation in North Kivu following the M23 mutiny and related ruthless attacks against civilians is extremely alarming," said Roger Meece, special representative of U.N. Secretary General Ban Ki-moon.
Meece was cited in a United Nations report issued in Geneva as saying a new round of systematic killings of villagers appeared to have occurred in early August.
U.N. High Commissioner for Human Rights Navi Pillay said allegations of hundreds of killings were still being verified, but preliminary investigations suggested that a large number of people, mainly women and children, had been slaughtered.
"The sheer viciousness of these murders is beyond comprehension," she said.
The Congo government in Kinshasa this month rejected calls by other countries in the region for an exclusively African force to tackle the insurgency in the east.
Congo says some of the insurgent groups have support from countries such as Rwanda and Uganda - a charge both governments deny - and wants an expansion of the 17,000-member U.N. peacekeeping force in the vast, mineral-rich state.
Pillay's office in Geneva said its mission in Congo had recorded 45 attacks on 30 North Kivu villages since May by a group dubbing itself "Democratic Forces for the Liberation of Rwanda" or FDLR, and another called Raia Mutumboki.
The FDLR is largely composed of ethnic Hutus, many of whom fled into the Congo after the defeat of a Hutu government widely viewed as responsible for the massacre of up to a million Tutsis and opponents of its policies in Rwanda in 1994.
The movement sometimes stages attacks in alliance with another armed group, Nyatura, the United Nations says.
Raia Mutumboki, largely composed of Congolese Tutsis but reinforced by others from Rwanda, according to the Congo government, says it is protecting the local population by attacking Hutus, whom it regards as foreigners.
The U.N. force, known as MONUSCO, focuses on protecting civilians but has been forced to divert resources to tackle the fallout from fighting between the Congolese army and M23.
That conflict has displaced nearly half a million people since the mutiny in April led to the formation of the rebel group that accuses Kinshasa of violating a 2009 peace accord.