The report surveyed the cause and consequence of a five-day wave of violence that erupted on June 10 in the southern city of Osh and led to the fleeing of at least 400,000 people to neighbouring Uzbekistan.
Large-scale "sweep" operations took place in Uzbek neighbourhoods, during which law enforcement officers beat and insulted residents and looted their homes, the report added.
The findings were based on 200 interviews with ethnic Kyrgyz and ethnic Uzbek victims and witnesses, lawyers, human rights defenders and government officials.
HRW also reported the torture and ill-treatment of more than 60 detainees, one of whom died of injuries sustained while in custody.
"In at least four cases, the victims reported being tortured by suffocation with gas masks or plastic bags put on their heads; one detainee reported being burned with cigarettes, and another reported being strangled with a strap."
A spokesman for the Kyrgyz prosecutor general's office rejected the allegations, saying the government was capable of investigating without outside assistance.
"We are capable of objectively investigating this by ourselves. Yes, there were offenses committed by the Kyrgyz security forces, but there was no genocide or ethnic cleansing of Uzbeks," Sumar Nasiz told AFP news agency.
Meanwhile, Farid Niyazov, Kyrgyzstan's interim government spokesman, did not immediately comment on the report, but said the government welcomes the probe and would continue to co-operate with rights groups to help establish the truth about the unrest.
Kyrgyzstan, an impoverished country bordering China, has been wracked by political chaos and ethnic violence since violent street protests toppled President Kurmanbek Bakiyev in April.
Roza Otunbayeva, the interim president, has struggled to impose order since assuming power, particularly in its deeply-divided southern regions.
Tensions between the two communities are believed to be rooted in a rivalry over land in the overpopulated Ferghana Valley, where the violence-wracked cities of Osh and Jalal'abad are located.
"The conflict is related to the lack of balance, as economic powers were in the hands of Uzbeks, while political power belonged to Kyrgyz," Anna Neistat, HRW researcher, said.