More than 1,500 deaths occurred at the hands of police over that period of time, the human rights organization said.
The police-involved deaths are "rarely investigated," the report said.
"Rio de Janeiro is a tale of two cities," said Atila Roque, the director of Amnesty International Brazil. "On the one hand, the glitz and glamour designed to impress the world and on the other, a city marked by repressive police interventions that are decimating a significant part of a generation of young, black and poor men."
The country's "very real drug and violence public security crisis is backfiring miserably," she said, adding that the Brazilian police are "corrupt" and "ill-resourced."
Rio's Secretary for Public Security José Mariano Beltrame criticized the report in a statement to CNN.
"I consider it reckless and unfair to publish the study of these cases at a time when the levels of criminality are falling in Rio," he said. The police have seized control from drug gangs in certain areas and established a permanent presence, he said, and in those areas there were only 20 police-involved killings in 2014, which he said was an 85% drop from 2008.
While there are areas in Rio that are "war zones," he said, he insisted that criminality overall has improved since 2007.
Amnesty said in its report that it asked the Rio de Janeiro Secretariat for Public Security for the investigation reports relating to all the killings described in the human rights' group report, but the request was denied.
The report is the latest in a series of controversies city and state officials are rushing to stamp out before the Games.
Rio de Janeiro Mayor Eduardo Paes told CNN the Olympics have given his city an opportunity to improve.
"We've still got a long way to go, a lot to do," he said. "It's a bit event. It's transforming completely the city, but I'm pretty optimistic things are going to go fine."
Crime long a problem in Brazil
When a police-involved killing occurs, according to Amnesty, a civil police officer files an administrative report to determine if the killing was in self-defense or if criminal charges are necessary.
The report says that police-involved killings are committed in the name of a war on drugs.
CNN has previously reported police raids in slums in order secure those areas ahead of the 2014 World Cup and for the Olympics.
Chronic crime and violence
have been problems in some parts of Brazil for years.
Rio de Janeiro was the state with the highest homicide rate in Brazil, Amnesty reports. In 2002, the homicide rate in the state as a whole was 56.5 per 100,000 inhabitants and in the capital it was 62.8. There was a significant reduction over the next 10 years, with the rates in the state and the capital falling to 28.3 and 21.5, respectively, although they are still well above the global homicide rate.
The murder rate in Brazil as a whole has risen 132% over the past 30 years but has dropped since reaching a peak in 2003, CNN reported in 2013
An October 2012 CNN story
highlighted a raid by 2,000 military troops and police in the slums of Jacarezinho and Manguinhos. Police said that they seized automatic weapons, guns and grenades and arrested scores of people, and that no one was injured.
In many cases that Amnesty said it examined, cases of police-involved killings are filed as "resistance followed by death." That classification system "prevents independent investigations and shields the perpetrators from the civilian courts," Amnesty contends.
Amnesty also found that crime scenes are "frequently altered," in that police officers remove a body "without due diligence" and plant items like guns as evidence next to body.
The research that was used in Amnesty's report was conducted between August 2014 and June 2015 and drew on primary and secondary data sources such as in the field reporting, interviews with victims and their families, witnesses, human rights defenders, civil society organization representative and specialists in public security.
Amnesty pulled data for overall homicides from the Ministry of Health, and examined cases involving police from 2005 through 2014 from the Institute of Public Security. Amnesty visited Acari 14 times to conduct interviews with more than 50 people in the community, including members of the police.
Acari was chosen as Amnesty's focus because, the report said, it had the greatest number of homicides resulting from police intervention.
Cases described in the report are based on interviews with slum residents who witnessed police-involved killings firsthand, other witnesses and family members as well as information gleaned from incident documents, death certificates, investigative reports, photos and videos, Amnesty said.
Other reports involving police
Amnesty's report is not the first time Brazilian police have been accused of extrajudicial killings.
Brazilian police killed more than 11,000 civilians from 2009 to 2013, according to a 2014 report by the Forum on Public Safety
, a group that collects and disseminates government safety data.
By comparison, the reports says, police in the United States killed roughly the same number of people over 30 years -- from 1983 to 2012.
The report concluded that "abusive use of lethal force" is used in Brazil.
A July 2015 paper
published in the academic journal Rio Police, commissioned to examine authorities' use of lethal force, offers no statistics on killings by officers. But the paper advocates for Rio's military police to reform its use of force practices by implementing the same model that United States federal agents use.
Brazilian police have endured many deaths, as well.
Last November, state media reported
that 100 military police had been killed in Rio in 2014 -- 17 on duty and 85 off duty.