Violence including gunfire and bombs caused the majority of deaths but thousands of people died from worsening health and environmental conditions directly related to the conflict that began in 2003, U.S. and Iraqi public health researchers said.
"Since March 2003, an additional 2.5 percent of Iraq's population have died above what would have occurred without conflict," according to the survey of Iraqi households, titled "The Human Cost of the War in Iraq."
The survey, being published online by British medical journal The Lancet, gives a far higher number of deaths in Iraq than other organizations.
Researchers randomly selected 1,849 households across Iraq and asked questions about births and deaths and migration for the study led by Gilbert Burnham of Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland.
They extrapolated the figures to reflect the national picture, saying Iraq's death rate had more than doubled since the invasion.
Iraqis "bear the consequence of warfare," the report said, comparing the situation to other wars: "In the Vietnam War, 3 million civilians died; in the Congo, armed conflict has been responsible for 3.8 million deaths; in East Timor, an estimated 200,000 out of a population of 800,000 died in conflict.
"Recent estimates are that 200,000 have died in Darfur [Sudan] over the past 31 months. Our data, which estimate that 654,965 or 2.5 percent of the Iraqi population has died in this, the largest major international conflict of the 21st century, should be of grave concern to everyone."
The researchers estimated that an additional 654,965 people have died in Iraq since the invasion above what would have been expected from the pre-war mortality rate. They did not ask families whether their dead were civilians or fighters.
Violence claimed about 601,000 people, the survey estimated -- the majority killed by gunfire, "though deaths from car bombing have increased from 2005," the study says.
The additional 53,000 people who are believed to have been killed by the effects of the war mostly died in recent months, "suggesting a worsening of health status and access to health care," the study said. It noted, however, that the number of nonviolent deaths "is too small to reach definitive conclusions."
Other key points in the survey:
The number of people dying in Iraq has risen each year since March 2003.
Those killed are predominantly males aged 15-44.
Deaths attributed to coalition forces accounted for 31 percent of the dead.
Although the "proportion of deaths ascribed to coalition forces has diminished in 2006 ... the actual numbers have increased each year."
The authors said their method of sampling the population is a "standard tool of epidemiology and is used by the U.S. government and many other agencies."
Professionals familiar with such research told CNN that the survey's methodology is sound.
Information for the survey was collected by Iraqi doctors, and analysis was performed by the faculty of the Johns Hopkins School of Public Health in cooperation with the Center for International Studies at Massachusetts Institute of Technology.
It has been very difficult to pin down fatality numbers during the Iraq conflict.
The private British-based Iraq Body Count research group puts the number of civilian deaths at between 43,850 and 48,693. Those figures are based on online media counts and eyewitness accounts.
"The count includes civilian deaths caused by coalition military action and by military or paramilitary responses to the coalition presence (e.g. insurgent and terrorist attacks)," the group's Web site says. "It also includes excess civilian deaths caused by criminal action resulting from the breakdown in law and order which followed the coalition invasion."
The latest estimates were released less than a month ahead of U.S. midterm elections that could change the balance of power in the House and Senate, now controlled by Republicans.
