A draft UN report says crimes by the Rwandan army and allied rebels in Democratic Republic of Congo could be classified as genocide.
The report, seen by the BBC, details the investigation into the conflict in DR Congo from 1993 to 2003.
It says tens of thousands of ethnic Hutus, including women, children and the elderly, were killed by the Tutsi-dominated Rwandan army.
Rwanda's justice minister has dismissed the claims as "rubbish".
The report also lists human rights violations committed by security forces from all the countries involved in what has been called "Africa's world war".
The final UN High Commission for Human Rights report should be made public in the next few days.
Although the conflict is officially over, eastern DR Congo, near the Rwandan border, remains volatile.
On Thursday, the UN Security Council held an emergency session to discuss allegations that Rwandan Hutu rebels were among armed men who raped at least 150 women and baby boys in the town of Luvungi and surrounding villages earlier this year.
The 545-page report, prepared by about 20 human right officers, documents what they call widespread and systematic attacks by the Rwandan army and the Congolese AFDL rebel movement.
The AFDL rebels were led by Laurent Kabila, father of current Congolese President Joseph Kabila.
Those targeted were Rwandan Hutus who had fled into what is now DR Congo, then called Zaire, after the 1994 genocide.
Rwandan Hutu extremists slaughtered some 800,000 ethnic Tutsis and moderate Hutus during the genocide.
Many of those responsible fled Rwanda as Tutsi rebels took power in Kigali in June 1994, taking hundreds of thousands of Hutu civilians with them.
But the report says that attacks against Hutus who were not refugees seem to confirm that Congolese Hutus were also targeted.
In some regions, it says, checkpoints were used to identify people of Hutu origin, and kill them.
Tens of thousands were killed, the report estimates, saying such acts suggest a premeditated and precise methodology.
"The extensive use of edged weapons... and the systematic massacres of survivors after [Hutu] camps had been taken, show that the numerous deaths cannot be attributed to the hazards of war or seen as equating to collateral damage," the report says.
It says such killings could amount to genocide "if proven by a competent court".
Rwanda's government has angrily dismissed the report - as it has previous charges that its Tutsi-dominated forces committed mass killings of Hutus in Rwanda after taking power to end the 1994 genocide.
It has always said its forces entered Zaire to pursue the Hutu militias responsible for carrying out the mass killings.
"It's a report by NGOs that has no basis," Rwanda Justice Minister Tharcisse Karagurama told the BBC's World Today programme.
"That's why it has been rejected outright, has no value, and all the countries which have been cited have rejected it."
"This report is mostly about the fight among Rwandese in our country," he said.
BBC West Africa correspondent Thomas Fessy, who has seen the draft report, reports that sources close to the investigation say that the Rwandan authorities have put pressure on the UN to tone down the report.
However, this was denied by Mr Karagurama.
France's Le Monde newspaper reported that Rwanda's President Paul Kagame has threatened to withdraw peacekeepers from the joint UN-African Union peacekeeping mission in Sudan's Darfur region over the report's allegations.
DR Congo expert Jason Stearns says the draft may have been leaked to prevent senior officials editing out the allegations of a possible genocide under Rwandan pressure.
He says the report will greatly tarnish the reputation of the current Rwandan government which prides itself on having brought to an end the genocide against Tutsis.
The UN investigators have also gathered information on alleged crimes committed by the security forces of many of the countries and armed groups involved in what became a regional war, involving at least nine countries and numerous rebel groups.