It says that those 33 per cent - the largest proportion of civilian deaths - were killed by illegal execution after abduction or capture.
Of that proportion, 29 per cent were found to have been tortured, with another 20 per cent dying from small arms gun fire and 14 per cent due to suicide bombs.
"On average for example, an air strike will kill 17 people - the majority of those killed will be women and children - but the number of air strikes recently has been quite small, whereas the number of executions has been very large," John Sloboda, from Iraq Body Count, which supplied the figures for the study, told Al Jazeera.
"There are enough incidents now available for us to be able to do these analyses which show very clearly that air strikes have the most indiscriminate effect on civilian population, but the number of individual incidents is greatest for executions and small arms fire."
The study, published in the New England Journal of Medicine on Thursday, said that executions had been "applied systematically and strategically to civilians in Iraq".
Iraq Body Count, which supplied the data for the study, publishes a database of violent civilian deaths caused by the 2003 military invasion and the breakdown of social order.
Research at the University of London focused on the Iraq Body Count data between March 20, 2003, and June 19, 2008 - a total of 91,358 Iraqi deaths.
The deaths include those caused by US-led forces and paramilitary or criminal attacks, and is cross-referenced by reviews of hospital and mortuary records, as well as figures from official bodies and non-governmental organisations.
From that number, about 10,000 deaths were excluded due to being caused by prolonged periods of fighting, for instance the two sieges of Fallujah in 2004.
Another 20,000 deaths were omitted, as they were not attributed to a particular cause of death.
Since the US-military "surge" against opposition fighters in Iraq, and the building of walls and checkpoints in the capital, the number of civilian deaths has dropped as resistance activities have been limited.