In April, Foreign Policy published a three-part series documenting the U.N.’s failure to properly report crimes against civilians and blue-helmet peacekeepers in Darfur, prompting calls from the International Criminal Court’s top prosecutor, Human Rights Watch, and other organizations for an independent investigation into allegations that the world body was trying to cover up evidence of a failing mission.

At the time, U.N. Secretary-General Ban Ki-moon declined to sign off on the request for an independent probe. But in July, the U.N. chief agreed to set up an internal U.N. probe headed by Phil Cooper, an American who formerly worked as a U.N. peacekeeping official, to review the allegations that U.N. and African Union peacekeepers had turned civilians over to armed rebels and covered up crimes by the Sudanese government, including lethal attacks against the blue helmets themselves.

The final report — which has not been made public in full — found five instances in which officials from the clumsily named African Union/United Nations Hybrid Operation in Darfur, also known as UNAMID, withheld evidence indicating the culpability of Sudanese government forces, or their proxies, in crimes against civilians and peacekeepers, according to a statement issued Wednesday by Ban’s spokesman, Stéphane Dujarric.

“The Secretary-General is deeply troubled by these findings,” Dujarric said. “He recognizes that UNAMID faces unique challenges owing to its complex mandate and operating environment. Nevertheless, keeping silent or underreporting on incidents involving human rights violations and threats or attacks on U.N. peacekeepers cannot be condoned under any circumstances.”

The report concluded that U.N. officials in Darfur, fearing reprisals from an often hostile Sudanese government, self-censored their reporting on Sudanese abuses, leading to “under-reporting of incidents when Government and pro-Government forces were suspected to be involved,” according to a five-page summary of the Cooper review distributed Wednesday to members of the 15-nation Security Council. Foreign Policy obtained a copy of that summary.

But Ban insisted that the report “did not find any evidence to support the allegation that UNAMID intentionally sought to cover up crimes against civilians and peacekeepers,” according to a three-page letter the U.N. presented to the Security Council along with the summary on Wednesday. And no individuals responsible for shortcomings were singled out in the summary or punished.

While the report’s summary echoes Ban’s conclusion that there was no evidence U.N. and African Union peacekeeping officials “intentionally” covered up crimes, it provides considerable circumstantial evidence suggesting they may have. For instance, the report concludes that UNAMID official failed to furnish U.N. headquarters with one report detailing attacks, rapes, and looting by pro-government forces at four villages in the Darfuri village of Tawilla. The mission also never informed New York that Sudanese government forces piloting an attack helicopter had threatened to attack a U.N. convoy. The U.N. mission also failed to identify Sudanese-backed forces as the suspected culprit in a bloody attack on Nigerian peacekeepers in the town of Muhajeria. “There was considerable evidence and reason to believe that the fatal attack on [the U.N.] team site was carried out by pro-Government forces,” according to the summary.

Aicha Elbasri is a U.N. whistleblower who first brought the scandal to light by providing Foreign Policy with thousands of pages of internal U.N. documents detailing the mission’s suppression of evidence of crimes by Sudanese soldiers and their proxies, including the murder of blue helmets. She denounced the U.N. findings as “an exercise in damage control.”

“This is not the ‘thorough, independent, and public inquiry’ the International Criminal Court called for in June,” added Elbasri, who cooperated with the U.N. review. “What we have here is just a cover-up of a cover-up.”

Elbasri, who served as U.N. chief spokeswoman for the Darfur mission, resigned from her job in April 2013 after claiming that she had been prevented from carrying out her responsibility of accurately informing the public about what was happening in Darfur. She said that she decided to share the internal documents with Foreign Policy after multiple efforts to raise her concerns within official U.N. channels failed to bring about change.

“I am not disappointed with the outcome of this review because I simply didn’t expect to hear the truth from an internal evaluation that lacks the minimum of transparency and independence that can lead to any credible findings,” she added.

The U.N. Security Council established UNAMID in 2008 to offer the promise of peace and security to the more than 2.7 million Darfuris driven from their homes by a Sudanese government-sponsored scorched-earth campaign that left hundreds of thousands dead from violence, disease, and malnutrition.

Khartoum has always resented the international presence, and it has attacked and intimidated the blue helmets with such ferocity that they have been largely incapable of fulfilling their mandate.

A summary of the Cooper review found deep flaws and faults in the U.N.’s administration of the mission, citing a “dysfunctional and deeply divided” press operation that labored over preparing routine releases and reports. U.N. and African Union peacekeepers — who have been subjected to more lethal attacks than any other U.N. peacekeeping mission, with nine killed in 2011 and 12 in 2012 — harbored a palpable fear of the government, leading to excessively deferential treatment.

“Maintaining civil relations and cooperation with the Government of the Sudan to ensure the Mission can fulfill its mandate to the best of its ability has become an end in itself,” according to the summary. “The period under review being only eight months could also not be seen in isolation from the events of the previous four years since the Mission’s establishment. Those years have left an atmosphere of intimidation and reticence by staff to report negatively on the government for fear of reprisals, such as travel restrictions and visa delays.” For instance, Sudan barred the top communications official from even entering Darfur to do his job.

In his letter to the U.N. Security Council, Ban expressed sympathy for the mission’s plight. But he said he was “troubled” by its failure to report honestly and fully about what was happening in Darfur. There was “a tendency on the part of the Mission not to report anything if not absolutely certain of the facts, even where there was enough evidence to make an informed judgment about the circumstances surrounding an incident,” he wrote, noting that all five underreported cases cited in the investigation “involved culpability of government or pro-government forces.”

“I recognize the unique challenges facing UNAMID, which has not always enjoyed the consent and cooperation of the Government of Sudan necessary to implement its mandate effectively,” Ban added. “Nevertheless, the lapses in the reporting standards of the Mission and its tendency not to report fully on incidents involving attacks on civilians and U.N. peacekeepers are very troubling.”

Human rights advocates said the release of the report should underscore the need for U.N. peacekeepers to take their jobs as watchdogs far more seriously — and not to silence themselves because of fears of possible repercussions.

“Whether or not you call it a cover-up, the report reveals a shocking failure to report on attacks on civilians, always it seems to the benefit of the government,” said Philippe Bolopion, Human Rights Watch’s U.N. representative. “This report should be a wake-up call to other U.N. missions, whether in Mali, CAR [the Central African Republic], Libya, or South Sudan, that proactive and transparent reporting on human rights violations, regardless of the perpetrators, is a core function of the mission, and one that the U.N. Secretary-General expects them to perform diligently.”

But Elbasri said she will keep pressing for U.N. officials to be held to account for their failings in Darfur. “What pushed me to resign my post and sacrifice my career and sole income isn’t just the U.N.-admitted ‘underreporting’ and ‘silence’ of UNAMID,” she said. “It is what the former chief of UNAMID, Ms. Aichatou Mindaoudou, had rightly described as a deliberate manipulation of all UNAMID reporting by two or three officials to serve some hidden agendas.”

“I stand by the charges I am pressing against both UNAMID and the Department of Peacekeeping Operations,” she added. “And I challenge the U.N. to establish an independent and public inquiry for the sake of the truth, the whole truth, and nothing but the truth.”