Forensic science experts examining mass graves in the Democratic Republic of the Congo could provide further evidence of a Tutsi-led retaliatory genocide of Hutu civilians in the mid-1990s.

A diplomatic row is raging over a draft of a UN report, leaked to the press late last month, that accuses Rwandan President Paul Kagame's troops of massacring Hutu refugees who had fled to neighbouring Zaire, now Congo, after the 1994 genocide in Rwanda of Tutsis and moderate Hutus that left 800,000 dead. The intervention of Kagame's forces has been credited with ending the 1994 killings.

The Rwandan government reacted furiously to the UN draft last week, calling it "outrageous" and describing its claims as "immoral". The government is now threatening to pull troops out of UN peacekeeping duties in protest. Many fear the UN will be forced to tone down the report when it is published, after some delay, next month.

Evidence is mounting that Rwandan forces, which were ordered by Kagame into Congo in pursuit of Hutu militias, may have taken systematic revenge on refugees, killing tens of thousands of civilians who had taken refuge in camps and villages across the border.

Killings of Hutus continued into the subsequent war, the Second Congo War, which ended in 2003, and the country is still scarred by conflict.

The Observer has learned that the leak of the report coincides with the completion of the training of the first team of Congolese forensic science investigators, which is being led by Peruvian forensic expert José Pablo Baraybar.

He gained international renown for his investigations in Srebrenica, where 8,000 Bosnian Muslims were murdered by Serbian forces in 1995. Baraybar's work there was crucial to the declaration that a genocide had taken place.

Baraybar, who has previously worked at exhumations in Haiti, Rwanda and Ethiopia, has spent three months training 40 carefully selected members of the police and the Congolese army in the province of North Kivu, eastern DRC, to "investigate their own dead".

He told the Observer that the apparent acknowledgment by the world of the massacres in Congo meant work could now start on uncovering the stories of the millions who had since died.

The UN draft report suggests that both Hutu DRC civilians and Rwandan Hutu refugees were being killed up until 2003 by the Rwandan armed forces and Congolese militias.

"Thanks to this new report by the UN we will be able to exhume the bodies that are spread throughout a country waiting for justice to be done for a community that has suffered a genocide, which has been silenced for over 10 years," said Baraybar.

The new Congolese forensic science team had been practising on cloth dummies in mock graves, he said.

"This was excellent training, very participatory," said Major David Bodeli Dombi, as he finished the two-week foundation course. "None of us can say we knew this material before we came."

The testimonies of more than 1,200 Hutus who survived attacks in Congo were collated by the authors of the UN report. Those accounts were corroborated by witnesses in North Kivu, interviewed by the Observer, who backed the claims of Rwandan atrocities.

One witness, Mukaru, a Hutu who was living in the Congolese village of Rutshuru in 1996 when the soldiers came, said: "The Rwandan army arrived in my village, and put us all in an enclosed space. They wanted to talk, they said. I was small and scared, and I didn't want to go. I ran off and hid, but my family and all the other villagers went in.

"A little while later they took them to the banana plantation and the massacre began. They cut off their heads, and hit them with hammers. They killed all of them, more than 400 people. Women, children, they all died. There was no one left, only me. I was 10 years old."

Emmanuel, from the same village,said simply: "I am a victim of genocide. They locked us into a large place and began to separate the men from the women. I thought I was going to die.

"There were about 300 of us in that room. They began to take us off in groups of 10 and I could hear gunshots outside. And no one came back. Then they took another 10 men, and then another 10. They did this 30 times. They were being executed. I had to escape." Thousands of Hutu were decapitated and their bodies thrown into trenches – just as the Hutu killers in Rwanda had done with their Tutsi victims.

In the provincial capital, Goma, police captain Wivine Emwendo has become one of the first female forensic science technicians in her country. She is aware of the importance of her role. "Soldiers and rebel groups have been humiliating and exterminating an ethnic group. I want to help bring those responsible to justice, and I now have the tools necessary to do this," she said.

Farther north in the town of Rubare, Herve Sabiarimana has created, with the help of the Peruvian Forensic Anthropology Team, a human rights centre which is compiling a list of the victims, essential data for identification and for the eventual prosecution of those responsible.

Herve said: "We already know where the mass graves are, a total of 49,000 people have been buried in this area alone, and we are now in the process of finding all possible data linked to the disappearances."

Outside the centre is 12-year-old Bamako who watched his entire family die at the hands of machete-wielding Rwandan soldiers. "My pain is so huge that I need to recover my dead so that I can bury them and weep for them. I don't want them to be left, buried like animals," he said.

Despite the fury of Rwandan politicians, the survivors of what may yet be declared a second genocide are eagerly awaiting recognition by the world of what their relatives and neighbours suffered. "Hope now lies in the heart of an entire people who have suffered in silence, suffering a systematic genocide that has gone unpunished," said Baraybar.

"A light seems to have appeared at the end of a dark tunnel of death. The new Congolese forensic team is ready, at last, to exhume its own dead."