Iraqi Health Minister Saleh al-Hasnawi 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 the conference call.
The White House said it had not seen the study, but mourned the deaths of Iraqi civilians.
"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," said White House spokesman Tony Fratto.
"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."
The U.S. Department of Defence said enormous precautions were taken to avoid civilian deaths and injuries.
More than half of the violent deaths documented in the WHO report occurred in Baghdad.
An average of 128 Iraqis suffered violent deaths every day in the first year following the invasion. The next year, an average of 115 were killed daily and 126 died from violence each day in the third year after the war started.
Estimates of Iraq's civilian deaths have been hampered by the lack of a well-functioning death registration system, the WHO said.
Some 3,915 U.S. and 174 British forces 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.
Death tolls have fallen in recent months as the number of violent attacks in Iraq has declined.
