The report, compiled by a 19-member task force, was released Monday by the Institute on Medicine as a Profession and the George Soros-funded Open Society Foundations.
Task force member Dr. Gerald Thompson, professor emeritus of medicine at Columbia University, said the report found "physicians were transformed into agents of the military and performed acts that were contrary to medical ethics and practice."
It called on the U.S. Defense Department and the CIA to adopt practices that allow doctors and psychologists to adhere to their ethical principles.
The report was based on a two-year review of records in the public domain. It detailed several ways in which medical professionals allegedly were forced to breach ethical standards that call for them to do no harm.
The task force said doctors and psychologists were forced to be involved in abusive interrogations, determining how to increase the disorientation of detainees, using medical information for interrogation purposes and the force-feeding of hunger strikers.
Military policies also prohibited the doctors from providing medical treatment after abusive treatment and from reporting abuses against prisoners, the report alleged.
The task force called for an investigation of medical practices in military prisons and the release of a Senate Intelligence Committee review on CIA practices.
The task force said "changed roles for health professionals and anemic standards" remain despite steps by the Pentagon to address concerns over such practices, the British newspaper The Guardian reported.
Both the CIA and Pentagon rejected the report's findings, the BBC reported.
CIA spokesman Dean Boyd said it contained "serious inaccuracies and erroneous conclusions," while Pentagon spokesman Todd Breasseale said the report had been prepared by people who did not have access to the prisoners or their medical records.
Breasseale maintained the detainees received medical attention "on par with the very best of the global medical profession."