At least 98 deaths occurred, with at least 34 of them suspected or confirmed murder and manslaughter (deliberate or reckless killing), the group of US lawyers told BBC television on Tuesday.
Their dossier claims that 11 more deaths are deemed suspicious and that between eight and 12 prisoners were tortured to death.
However, charges are rare and sentences are light, the report said.
The report comes a week after new photographs of alleged prisoner abuse at Baghdad's US-run Abu Ghraib prison emerged.
The report alleged that one person was made to jump off a bridge into the Tigris river in Iraq and another forced inside a sleeping bag and suffocated.
The number of deaths in custody discounts those due to fighting, mortar attacks or violence between detainees. They were directly attributable to their detention or interrogation in American custody, the BBC's Newsnight programme said.
The report's editor Deborah Pearlstein told Newsnight: "We're extremely comfortable with the veracity and the reliability of the facts here.
"These are documents based on army investigative reports, documents that we've obtained from the government or that have come out through freedom of information act requests in the United States."
"These are documents based on army investigative reports, documents that we've obtained from the government or that have come out through freedom of information act requests in the United States"
Human Rights First organisation
Newsnight was told by the US Pentagon: "We haven't seen the report yet. Where we find allegations of maltreatment we take them very seriously and prosecute."
Zalmay Khalilzad, the US ambassador to Iraq, told the BBC: "There are thousands of prisoners that have been held by the coalition during the past more than two years.
"Some have died of natural causes and there have been charges of abuse. Of course, we always investigate and determine what happened and appropriate punishment is given if the judgment is made that illegal actions took place.
"If those reports are true, of course they would be terrible abuses and they would be illegal things. Those who are responsible for them would be investigated and they will be punished."
However, David Rivkin, a former White House legal adviser, said the numbers had to be put in perspective.
"[If] 10 people were tortured to death out of over 100,000 detainees in Iraq and Afghanistan" that was "a better rate" than in both world wars and "most civilian penal systems".
"It is not a scandal. Bad things happen in detention. A lot of them died for reasons that have nothing to do with it."
Amnesty International UK demanded an investigation into the deaths.
A spokesman said: "We want to see the US and its allies allowing a full independent and impartial investigation into these deaths, as well as mounting incidents of alleged torture and other mistreatment.
"We've also raised with the Americans the question of overly lenient sentences for those found guilty of torturing prisoners to death in Afghanistan."