A draft U.N. report on war crimes in Congo has raised the possibility that Rwandan President Paul Kagame, the former rebel leader who is widely credited with ending the Rwandan genocide, bore responsibility for war crimes and genocide that resulted in the deaths of tens of thousands of Hutu civilians during the late 1990s and were allegedly committed by troops under his command.

But did U.N. Secretary-General Ban Ki-moon seek to remove any mention of genocide in the report in response to a threat by Kagame's government to withdraw Rwanda's peacekeepers from U.N. missions? Ban is said to fear that such a move by Rwanda would doom the mission and cripple U.N. efforts to protect civilians in Darfur, according to senior U.N. officials

The U.N's sweeping, 545-page "mapping exercise," initiated in 2005 during the tenure of Ban's predecessor, Kofi Annan, in 2005, details more than 600 mass killings committed in Congo, formerly known as Zaire, from 1993 to 2003 and claims that the "systematic and widespread attacks described in this report reveal a number of damning elements that, if proven, could be classified as crimes of genocide." The report's preliminary findings have prompted Rwanda, which is identified as a key alleged perpetrator, to threaten to withdraw its troops from five U.N. peacekeeping missions, including the mission in Darfur.

Ban's press office and a spokesman for the U.N. High Commissioner for Human Rights, Navi Pillay, have denied an article in Le Monde alleging that Ban pressured Pillay to scrub the word genocide form the report. "I want to make this crystal clear: This is absolutely untrue," said Rupert Colville, Pillay's spokesman. "Up to this point the secretary general has never put pressure on the high commissioner to alter the text."

But officials tell Turtle Bay that while Ban's top advisors never directly asked Pillay to remove the word genocide from the report, they voiced strong concern about its inclusion in the document and asked her to conduct a legal review to ensure she had the basis to back up the charge.

According to U.N. officials, Ban's chief of staff, Vijay Nambiar, voiced misgivings to Pillay in a phone conversation late last month about the legal basis for the genocide assertion in the report, noting that the Rwandan government arranged for the repatriation of hundreds of thousands of ethnic Hutu refugees, the victims of the alleged genocide. Nambiar appealed to Pillay to have her lawyers revisit the issue to make sure that they could support such a serious charge. But he apparently made no direct request for her to remove the word "genocide" from the report, the officials said.

The U.N.'s top peacekeeping officials, including Under Secretary-General Alain Le Roy, also voiced concern to Pillay and her advisors in a series of meetings about the impact the findings would have on their efforts to ensure Rwanda maintains its involvement in Sudan as the country faces a politically sensitive referendum next year to determine whether the autonomous south will declare its independence. But they said they were essentially resigned to face the consequences of the Congo report.

A final version of the report -- whose release has been delayed till Oct. 1 to give Rwanda and other governments accused time to respond -- will continue to raise the possibility that Rwanda and several other countries, including Uganda, Burundi, and their Congolese allies, committed war crimes and possibly genocide in the 1990s, according to three U.N. officials familiar with the report.

But it will also make it clear that a final judgment can only be made by a court, and note that there is also evidence to suggest that a genocide did not occur, including Rwanda's repatriation of Hutus.

The final version had been revised to "tighten" some of the legal reasoning surrounding the genocide claim, but that there has been no "deliberate effort to excise or expunge certain phrases or words," according to a senior U.N. official. "We may have put it little more bluntly [in the original draft]. Now it's more specific. More nuanced."

The crisis erupted at a time when Ban has been seeking to repair the U.N.'s troubled relationship with Rwanda. Despite advance knowledge of the war crimes findings against Rwanda, Ban appointed Kagame, along with Spanish President Jose Luis Zapatero, as co-chairs of a special advisory group to promote the Millennium Development Goals (MDGs), which call on governments to sharply reduce poverty and combat other social problems by 2015.

The controversial appointment has triggered protests in Spain, where about 40 Rwandan military officials have been indicted for war crimes allegedly perpetrated in Rwanda in the 1990s. Bowing to the criticism, in July, Zapatero declined to attend his first scheduled meeting with Kagame in Madrid to discuss efforts to promote the millennium goals. He met only with Ban.

It remains unclear whether Zapatero will boycott a second meeting later this month on the sidelines of a major U.N. summit on the MDGs. "We knew it was coming," a senior U.N. official said of the Congo report's findings. "We didn't feel it would go so far and become such a controversy. We looked upon this in terms of Rwanda's record on the MDGs."

"Rwanda has displayed extraordinary commitment to the MDGs and is among the few countries in Africa that have made the most progress towards the goals," said Farhan Haq, Ban's deputy spokesman. "There have been commendable declines in both child and maternal mortality there. The country has also made remarkable progress in reducing the number of reported malaria cases and deaths and has the highest proportion of women parliamentarians in the world."

Ban is also considering Rwanda's foreign minister, Louise Mushikiwabo, to head a new U.N. super agency dealing with women's issues. Mushikiwabo vigorously defended Rwanda's human rights record in a letter to Ban, describing the U.N.'s inquiry into Rwanda's role in war crimes as "apocryphal," "fatally flawed" and an "embarrassment to the United Nations."  She said it was "patently absurd for the U.N., which deliberately turned its back on the Rwandan people during the 1994 genocide, to accuse the army that stopped the genocide of committing atrocities in the Democratic Republic of Congo."

Mushikiwabo has saved her sharpest criticism for former Secretary-General Kofi Annan, who was a senior U.N. peacekeeping official during the Rwandan genocide. The mapping exercise into war crimes in Congo was launched under Annan's tenure. "I want to say that his as far as Rwanda and the genocide [is concerned] is pitiful," she said at a recent press conference this week. He "has never taken his responsibility" for failing to confront the perpetrators of genocide. In contrast, Mushikiwabo praised Ban in her letter for leading the United Nations with "honesty, integrity and transparency."

Follow me on Twitter @columlynch.