The United Nations has accused Rwanda of wholesale war crimes, including possibly genocide, during years of conflict in the Democratic Republic of Congo.

An unprecedented 600-page investigation by the UN high commissioner for human rights catalogues years of murder, rape and looting in a conflict in which hundreds of thousands were slaughtered.

A draft version of the report, revealed by Le Monde and expected to be published next month, says the abuses, over a period of seven years and two invasions by Rwanda, amount to "crimes against humanity, war crimes, or even genocide" because the principal targets of the violence were Hutus, who were killed in their tens of thousands.

Among the accusations is that Rwandan forces and local allies rounded up hundreds of men, women and children at a time and butchered them with hoes and axes. On other occasions Hutu refugees were bayoneted, burned alive or killed with hammer blows in large numbers.

It is the first time the UN has published such forthright allegations against Rwanda, a close ally of Britain and the US.

The Rwandan government reacted angrily to the report today, dismissing it as "amateurish" and "outrageous" after reportedly attempting to pressure the UN not to publish it by threatening to pull out of international peacekeeping missions. Rwanda's Tutsi leaders will be particularly discomforted by the accusation of genocide when they have long claimed the moral high ground for bringing to an end the 1994 genocide in their own country. But the report was welcomed by human rights groups, which called for the prosecution of those responsible for war crimes.

The report by the Office of the High Commissioner of Human Rights (OHCHR) covers two periods: Rwanda's 1996 invasion of the country then called Zaire in pursuit of Hutu soldiers and others who fled there after carrying out the 1994 genocide of hundreds of thousands of Tutsis, and a second invasion two years later that broadened into a regional war involving eight countries.

Rwanda's attack on Zaire in 1996 was initially aimed at clearing the vast UN refugee camps around Goma and Bukavu, which were being used as cover by Hutu armed forces to continue the war against the new Tutsi-led government in Kigali.

Hundreds of thousands of the more than 1 million Hutus in eastern Zaire were forced back to Rwanda. Many more, including men who carried out the genocide but also large numbers of women and children, fled deeper into Zaire. They were pursued and attacked by the Rwandan army and a Zairean rebel group sponsored by Kigali, the AFDL.

The UN report describes "the systematic, methodical and premeditated nature of the attacks on the Hutus [which] took place in all areas where the refugees had been tracked down".

"The pursuit lasted months and, occasionally, humanitarian aid intended for them was deliberately blocked, notably in the eastern province, thus depriving them of things essential to their survival," the report said.

"The extent of the crimes and the large number of victims, probably in the several tens of thousands, are demonstrated by the numerous incidents detailed in the report. The extensive use of non-firearms, particularly hammers, and the systematic massacres of survivors after camps were taken prove that the number of deaths cannot be put down to the margins of war. Among the victims were mostly children, women, old and ill people."

The report goes on to say that "the systematic and widespread attacks have a number of damning elements which, if proved before a competent court, could be described as crimes of genocide".

The UN also adds that while Kigali has permitted Hutus to return to Rwanda in large numbers, that did not "rule out the intention of destroying part of an ethnic group as such and thus committing a crime of genocide".

The Zairean army collapsed in the face of the invasion and Rwanda seized the opportunity to march across the country and overthrow the longstanding dictator, Mobutu Sese Seko. Laurent Kabila was installed as president. He promptly changed the name of the country to the Democratic Republic of Congo (DRC).

Rwanda invaded again in 1998 after accusing the new regime of continuing to support Hutu rebels. The following five years of war drew in armies from eight nations as well as 21 rebel groups in a conflict that quickly descended in to mass plunder of the DRC's minerals as well as a new wave of war crimes.

The UN report accuses Angolan forces of using the cover of the war to attack refugees from Angola's conflict-plagued Cabinda province who had fled to the DRC. Angola is accused of "executing all those they suspected of colluding with their enemies". Angolan soldiers also raped and looted, the UN investigation said.

International human rights groups welcomed the UN report and said it should be used to bring the accused to trial. "This is a very important report," said Human Rights Watch. "We hope that it can form the basis for ending the impunity that has protected the people responsible for some of these crimes."

The UN's damning conclusions will prove hugely embarrassing to Rwanda, which is attempting to project itself as a rapidly modernising state that has put its brutal recent history behind it.

President Paul Kagame's office attempted to dismiss the report. "It's an amateurish NGO job, and it's outrageous," said a spokeswoman, Yolande Makolo. "Nobody reasonable believes that it's helpful to anybody. The countries mentioned in the draft report have rejected it and will continue to reject it."

Makolo did not comment on reports that Kagame last month warned the UN secretary general, Ban Ki-moon, that Rwanda would pull its troops out of peacekeeping missions in Darfur and elsewhere if the report was made public. Le Monde said that threat was reiterated in a letter to Ban by Rwanda's foreign minister, Louise Mushikiwabo.

Rupert Colville, spokesman for the UN high commissioner for human rights, said the leaked draft was not the final version and the report to be published next month had undergone revisions.

"It's only a draft from about two months ago and the proper final version will come up very soon," he said.

But if there are substantial differences, the UN is likely to stand accused of bowing to pressure from Rwanda.

Atrocities detailed in the OHCHR document seen by Le Monde

Kinigi, 7 December 1996 "Elements from the AFDL/APR killed nearly 310 civilians, many of them women and children. The troops had accused the local population, mostly Hutu, of sheltering Interahamwe [Hutu paramilitaries, who] had already left the village. At first the troops sought to reassure the civilians [whom they gathered together] in several buildings, including the adventist church and the primary school. In the afternoon, troops entered these buildings and killed the villagers with hoes or axes to the head."

Luberizi, 29 October 1996 "Elements from the AFDL/APR/FAB [Burundi's armed forces] killed around 200 male refugees. The victims were part of a group of refugees told by the troops to regroup so that they could be repatriated to Rwanda. The troops separated the men from the rest of the group and killed them with bayonets or bullets. The bodies were then buried in mass graves [near to] the church."

Bwegera, 3 November 1996 "They burned alive 72 Rwandan refugees in Cotonco (cotton company) headquarters, one kilometre from the village."

Mutiko, December 1996 "Special units from the AFDL/APR started to hunt down refugees, killing several hundred. Once they had been intercepted at barriers put up by the troops, the victims were given food and told to get into UN lorries waiting at the exit of the village. The victims were then taken out on to the road, then killed with blows to the head with canes, hammers and axes. The troops encouraged the local population to take part in the killings."

• This article was amended on 27 August 2010. A heading in the timeline above suggested that the human rights report came from the UNHCR. This has been corrected.