The draft of the critical internal U.N. report says "events in Sri Lanka mark a grave failure of the U.N.," the BBC, which received the leaked document, reported.
It said the United Nations neglected to publicize the extent of casualties and deaths of civilians caught between the advancing Sri Lankan government army and retreating Tamil Tiger rebels in early 2009.
An earlier U.N. document, the 2011 U.N. Panel of Experts Report, claimed about 330,000 civilians were trapped.
The Tigers were fighting for a separate homeland for Tamils in northeastern Sri Lanka, an island nation several miles off the southern tip of the Indian subcontinent.
The PoE report said retreating Tiger rebels forced civilians to accompany them, shooting many people who tried to escape. Meanwhile, indiscriminate government shelling of rebel territory killed civilians.
The BBC said the latest internal U.N. report criticized senior U.N. management for deciding to pull out of the areas of conflict in the final days of the 26-year war that left an estimated 100,000 people dead.
The Sri Lankan government had a "stratagem of intimidation," including the "control of visas to sanction staff critical of the state," the BBC report said.
The "systemic failure" of the United Nations was its adoption of "a culture of trade-offs" whereby the organization decided to censor its criticism of the Sri Lankan government in order to get better access for its humanitarian efforts.
With the United Nations no longer in rebel-held territories during the final onslaught by government forces, it was left to the International Red Cross, whose staff members were in the area, to report what it said was an "unimaginable humanitarian catastrophe."
The BBC said former senior U.N. official Charles Petrie, who headed the U.N. report's internal review panel, that the draft seen by the BBC "very much reflects the findings of the panel" and he will present it to U.N. Secretary General Ban Ki-moon.
One U.N. team member, Benjamin Dix, who left the rebel area, told the BBC he was against pulling out.
"I believe we should have gone further north, not evacuate south, and basically abandon the civilian population with no protection or witness," the BBC quoted Dix as saying.
"As a humanitarian worker, questions were running through my mind 'what is this all about? Isn't this what we signed up to do?'"
Since the war ended there has been an uneasy relationship between former rebels, their leaders and the military as they attempt to reconcile differences and bring ex-Tamil Tigers into mainstream Sri Lankan life.
A major problem is agreeing how many former rebels, still held in remote camps, will be allowed into the regular army.
In February Sri Lanka's military appointed a five-member Court of Inquiry to look into civilian deaths allegedly at the hands of the army during the civil war.
The government set up a Lessons Learnt and Reconciliation Commission after the war that has reported on issues of integration.
However, the military and government repeatedly denied accusations of torture and indiscriminate bombing and killing of civilians.
In April 2011, the government slammed the 2011 U.N. Panel of Experts Report, saying it could kindle nationalistic flames and destroy trust on both sides of the Sri Lankan conflict.
"Among other deficiencies, the report is based on patently biased material which is presented without any verification," the External Affairs Ministry said in a statement at the time.