The report, by the Washington-based New America Foundation, will fuel growing criticism of the use of unmanned drones in the fight against al-Qaeda and Taliban militants, who use Pakistan as a base for attacks on Nato forces in Afghanistan.
Critics say their use not only takes innocent lives, but amounts to unlawful extra-judicial killing of militants.
The report by Peter Bergen and Katherine Tiedemann found that 32 per cent of those killed in drone attacks since 2004 were civilians.
Their report, The Year of the Drone, studied 114 drone raids in which more than 1200 people were killed. Of those, between 549 and 849 were reliably reported to be militant fighters, while the rest were civilians.
"The true civilian fatality rate since 2004 according to our analysis is approximately 32 per cent," the foundation reported.
The number of drone attacks has increased dramatically since Barack Obama replaced George W Bush as US president early last year.
There were 45 drone attacks during Mr Bush's two terms of government, compared with 51 during the first year of Mr Obama's new administration. In the first two months of this year, up to 140 "militants" have been killed.
Despite the controversy surrounding the scale of civilian deaths, and public opposition from Pakistan's government, the Obama administration has increased its reliance on drones to target "high-value" Taliban and al-Qaeda figures.
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Since last autumn, they have killed the Taliban's notorious leader Baitullah Mehsud in South Waziristan, and more recently, it is claimed, his successor Hakimullah Mehsud.
In 2008, Pakistani intelligence sources said they had killed Rashid Rauf, the British al-Qaeda militant behind the 2006 transatlantic airliner bomb plot.
Osama bin Laden's deputy Ayman al Zawahiri is believed to had a lucky escape when a drone struck a compound he had recently left.
Taliban leaders this week confirmed another of their top leaders Mohammed Qari Zafar had been killed in north Waziristan.
He was believed to have organised the 2006 bombing of the American embassy in Karachi.
The report said although civilian casualty figures are high, they did not believe their study would cause American commanders to reconsider their use.
"Despite the controversy drone strikes are likely to remain a critical tool for the United States to disrupt Al Qaeda and Taliban operations and leadership structures," it concluded.