While well below that figure, WHO's estimate exceeds the widely-cited 80,000 to 87,000 death toll by the human rights group Iraq Body Count, which uses media reports and hospital and morgue records to calculate its tally.
However, Mohamed Ali, a statistician for WHO, who co-authored the study, said: "There are a lot of uncertainties in making such estimates."
He said insecurity made parts of Baghdad and Anbar provinces unreachable for those conducting the survey.
Many families also fled their homes as a result of the violence, and some left the country, making it hard to give a precise assessment of the violence in Iraq.
As a result, Ali said the margin of error for the toll was relatively high.
But, he said the household survey's large scale gave the findings more weight than previous attempts to estimate the number of Iraqis killed in battles between and among military forces, opposition fighters and sectarian groups.
The John Hopkins University report, published by the British medical journal Lancet, which was based on a smaller-scale Iraqi survey, drew criticism from the White House and elsewhere for appearing to exaggerate the Iraqi death rate.
Saleh al-Hasnawi, Iraq's health minister, described the latest WHO report as "very sound" and said the survey indicated "a massive death toll since the beginning of the conflict".
"I believe in these numbers," he told reporters.
The White House said it had not seen the study but blamed "extremist" elements for the deaths.
Tony Fratto, a White House spokesman, said: "The unmistakable fact is that the vast majority of these deaths are caused by the wilful, murderous intentions of extremists committed to taking innocent life.
"It is also beyond dispute that more Iraqi citizens would be condemned to death and oppression if they were abandoned by America and our coalition partners."
More than half of the violent deaths documented in the WHO report occurred in Baghdad.
An average of 128 Iraqis were killed violently every day in the first year following the US invasion. About 115 people were killed daily the second year, while the third saw the average rise to 126 people dying every day.
The WHO said accurate estimates of Iraq's civilian deaths have been impaired by the lack of a well-functioning death registration system.
About 4,000 US and 174 British soldiers have died since the war began.
Between 4,900 and 6,375 Iraqi military personnel are thought to have died, though no reliable official figures have been issued since new security forces were set up in late 2003.
Deaths are reported to have fallen in recent months as the number of violent attacks in Iraq have declined.