The Human Rights First organisation, a group of US lawyers, told BBC television's Newsnight program that at least 98 deaths have occurred, with at least 34 of them suspected or confirmed homicides.
The report said 11 more deaths are deemed suspicious and between eight and 12 prisoners were tortured to death.
The Pentagon told Newsnight it has not seen the report, however takes allegations of maltreatment "very seriously and prosecute".
"We're extremely comfortable with the veracity and the reliability of the facts here," the report's editor Deborah Pearlstein told Newsnight.
"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."
The report said the number of deaths in custody discounts those due to fighting, mortar attacks or violence between detainees, and those counted are deaths directly attributable to their detention or interrogation in American custody.
It says one person was allegedly made to jump off a bridge into the Tigris River, and another was forced inside a sleeping bag and suffocated.
Doctor 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."
He said while most troops behaved according to the law, abuses did exist.
"They are human beings, they violate the law, they make mistakes and they have to be held accountable and the good thing about our system is that we do hold people accountable," he said.
The report comes a week after SBS' Dateline program aired previously unseen pictures showing apparent US abuse of prisoners at Iraq's Abu Ghraib jail in 2003.