"Around the world, the United States has been humiliating Muslim detainees by offending their religious beliefs," said Reed Brody, special counsel for the New York-based watchdog on Wednesday.
Newsweek on Monday retracted an article quoting an unidentified US official as saying that a probe into allegations of prisoner abuse at Guantanamo found that interrogators had thrown a Quran into a toilet to rattle Muslim prisoners.
The weekly magazine said the sole anonymous source had "backed away" from the account.
Brody said condemnation of the Newsweek article, which sparked anti-US protests in Afghanistan and other countries that left at least 14 dead, had been so vocal as to drown out documented complaints of similar mistreatment.
He said Human Rights Watch (HRW) had heard allegations that US interrogators disrespected the Quran from several former detainees, including three Briton and a Russian.
And Erik Saar, a former Army translator at Guantanamo, has said that guards routinely tossed the Quran on the ground, Brody said. Saar also described a female interrogator wiping a detainee with what the prisoner was made to believe was menstrual blood.
HRW argued that the Newsweek story would not have resonated had it not been for "extensive" US abuse of Muslim detainees and the government's failure to fully investigate all of those implicated.
"If the United States is to repair the public relations damage caused by its mistreatment of detainees, it needs to investigate those who ordered or condoned this abuse, not attack those who have tried to report on it," said Brody.