Human Rights Watch says it is likely crucial evidence for the trials of Saddam Hussein and other former Iraqi officials has been lost or tainted.
US-led coalition forces failed to secure relevant sites after last year's invasion of Iraq, the group says.
They failed to prevent people from looting thousands of official documents from government buildings.
The US-based human rights organisation has published a 41-page report entitled Iraq: the State of the Evidence.
Saddam Hussein is expected to go on trial some time next year
Coalition forces also failed to stop relatives of some of the many thousands of people who disappeared during Saddam Hussein's rule from digging up remains found at some mass grave sites, the organisation says.
Human Rights Watch says the availability of solid documentary and forensic evidence will be a key to the success of any trials in Iraq, corroborating and providing extra weight to witness testimonies.
But it says it is likely some evidence has been tainted or lost because of inaction or negligence by US-led coalition forces.
Human Rights Watch alleges that the coalition's failure to prevent or minimise the looting and destruction of government buildings in April 2003 led to the widespread removal of state archives, which are now virtually impossible to trace.
The coalition subsequently failed to put in place expertise and assistance needed to ensure proper classification and exhumation procedures.
In some areas, it says, coalition soldiers watched as villagers or families of people who disappeared during Saddam Hussein's rule dug up remains at mass grave sites.
The unprofessional manner in which the graves were unearthed, says the group, made it impossible for many relatives to identify the remains, or to keep those remains intact and separate.
Crucial evidence necessary for future trials was never collected and may have been irreparably damaged.
Human Rights Watch urges Iraq's interim government to set up a join Iraqi and international commission for missing persons to establish effective procedures for protecting mass graves and conducting exhumations, and a similar body to oversee the handling of documents of the former government.