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A Rwanda Patriotic Front (RPF) rebel is seen in front of the site of the plane crash which killed Rwandan President Juvenal Habyarimana in Kigali in this May 23, 1994 file photo.

JEAN MARC BOUJOU/ASSOCIATED PRESS

A United Nations criminal tribunal was so hobbled by the hostility of the Rwandan government that it was unable to investigate "very credible allegations" of crimes by the forces of President Paul Kagame, says Louise Arbour, the tribunal's former chief prosecutor.

Ms. Arbour, a retired Supreme Court of Canada justice, revealed details in an interview with The Globe and Mail of how the Kagame government and its supporters made it difficult for the International Criminal Tribunal for Rwanda to investigate many serious crimes, including the assassination of two presidents – the event that ignited the genocide in which 800,000 Tutsis and moderate Hutus were killed.

The attack on the presidential plane in 1994 was just one of many unsolved crimes in Rwanda before and after the genocide, she said, adding: "I think that remains a very serious failing of international criminal justice."

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Related: Rwandan president Paul Kagame feted in Toronto despite controversy

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Read more: Probe revisits assassination that triggered Rwandan genocide

Ms. Arbour's revelations about her three-year stint as the tribunal's chief prosecutor came after The Globe obtained two documents – a deposition by one of Mr. Kagame's former top aides and an earlier report by investigators at the UN Rwanda tribunal – pointing to the involvement of Mr. Kagame's forces in the death of Rwandan president Juvénal Habyarimana.

The missile strike on the night of April 6, 1994, that killed Mr. Habyarimana and Burundian president Cyprien Ntaryamira remains a mystery, but investigating magistrates in France have now reopened their probe to consider the new deposition by the former Kagame aide, who says he heard Mr. Kagame and two other aides admitting that they orchestrated the attack.

The French investigation was precipitated by a case filed by the families of the French crew of the plane carrying the two presidents, but later went into limbo because of a lack of witnesses.

Mr. Habyarimana's daughter Marie-Rose, now a Canadian citizen, has criticized the UN tribunal for failing to pursue charges in connection with the assassination. "People have closed their eyes," she told The Globe in an interview this month.

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But Ms. Arbour said in her interview that Mr. Kagame's government "could turn on and off the co-operative tap at will, depending whether they were pleased or not with the work that was being done."

The tribunal, which closed last December after more than two decades of work, indicted 95 suspects and convicted 61 of them, but all were linked to the former Hutu regime of Mr. Habyarimana, which was driven out of power by Mr. Kagame's forces after the genocide. Critics have said the tribunal became a form of "victor's justice."

The tribunal had the power to investigate crimes during the entire year of 1994, including the period before and after the genocide, but it did not indict anyone linked to Mr. Kagame and his Tutsi-led forces, despite many allegations against them.

"These kinds of very credible allegations have been made time and again," Ms. Arbour said. "And in the 22 years of its history, the tribunal has never been able to take that on."

The concerns about the imbalance in the tribunal's prosecutions are valid, she said.

Ms. Arbour disclosed that she had told her successor, Carla Del Ponte, that the tribunal "had to make some efforts" to investigate "serious allegations of crimes" by "elements or sympathizers" of Mr. Kagame's forces.

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Those investigations "could only be done from outside the country" because of the dangers and difficulties of working inside Rwanda, she told Ms. Del Ponte in 1999, when she left the tribunal to become a Supreme Court justice.

"The office of the prosecutor was sitting right in the middle of the country, where allegedly some of the leadership elements had to be investigated," Ms. Arbour told The Globe. "That's not, frankly, very doable."

Asked whether the tribunal could have investigated the assassination of the two presidents in 1994, she said: "We worked in a very fragile environment. I had a lot of concerns about the safety, the security of our witnesses. I don't think we had anywhere near the kind of human resources, capacity, know-how, to do that work while we were sitting in that country."

She drew a comparison to the criminal tribunal for the former Yugoslavia, where she was also the chief prosecutor and where she indicted former Yugoslav president Slobodan Milosevic for war crimes.

"I don't think we would have managed to do leadership investigations in Yugoslavia had we been, in a sense, hostage to the government of Croatia, Bosnia or Serbia," she said.

"Without being able to operate safely from the outside [of Rwanda] with a lot of credible, independent, outside investigative support – it's not an excuse, but it's in part an explanation as to why maybe this has never been done. It certainly would not have been doable in the first few years of the tribunal."

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The tribunal was "constantly in a conflictual position vis-à-vis President Kagame," she said. For example, his government insisted that some genocide suspects should be put on trial domestically in Rwanda, rather than sent to the tribunal's court in neighbouring Tanzania, she said.

"So even in the genocide prosecutions, we were very often – regularly – in conflict with the government, whom we would have thought would have been supportive of our work. So you can imagine what kind of situation we would have been in, sitting in the country needing visas to come in and out. … None of that was feasible without the full co-operation of the government."

In a forthcoming book by freelance writer Judi Rever, a former senior official at the Rwanda tribunal says it was difficult to ensure the safety of witnesses who had information incriminating Mr. Kagame.

"The problem was that witnesses kept disappearing," says Douglas Marks Moore, now a judge in Britain who was senior counsel to a team of investigators at the tribunal.

Many witnesses against Mr. Kagame fled to neighbouring countries such as Kenya and Uganda, but were then "extracted, tortured and killed," he says.

This led to a serious depletion of the witness pool, he says in Ms. Rever's book, In Praise of Blood, to be published by Random House Canada.

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Mr. Marks Moore says it was "unwise" for the tribunal to have prosecuted only "one side" of the crimes in Rwanda.

Another senior investigator at the tribunal, former U.S. Federal Bureau of Investigation agent Jim Lyons, told Ms. Rever that in 1997 the investigators heard detailed evidence from three witnesses who said Mr. Kagame was involved in planning the missile attack that killed the two presidents.

In the forthcoming book, Mr. Lyons says one of the tribunal investigators, Michael Hourigan, took the information to Ms. Arbour in 1997. "Arbour told him to shut down the investigation, that the ICTR had no mandate to investigate the plane crash – it had no jurisdiction," he says.

Ms. Arbour said she met Mr. Hourigan only once. The information that he brought her about the plane crash "didn't fall, in my view, within our prosecutorial agenda," she told The Globe. "I don't think we had the capacity or the resources, even if I had otherwise felt that we should collect information."

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