The National Episcopal Conference of the Congo (CENCO) report said officers used "disproportionate" force during an outbreak of street protests against the extended rule of President Joseph Kabila.
Fifty-two people were shot dead and one other died from tear gas over the sixth month period, according to 200 observers who monitored the protests for CENCO. Three police officers were killed by demonstrators.
The report also found that at least 105 people were injured -- 87 of them with bullet wounds -- and at least 335 protesters arrested by the police, armed forces and security services.
"The use of disproportionate force by the police and other state agencies is the basis for at least 98.67 percent of human rights violations" during the protests, the report said, adding that demonstrators should also "avoid all acts that could undermine public order".
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The Congolese government defended the actions of the police and questioned the legitimacy of the report for its "malicious intent or lack of professionalism".
"This report by CENCO only gives the time parameters without specifying the places where these acts occurred", Congolese government spokesman, Lambert Mende, told AFP.
But as protests and a bloody crackdown swelled, a deal was brokered by the Catholic Church enabling him to stay in office pending elections to be held by the end of 2017.
That election has now been delayed until December 23, 2018, and opposition and citizen movements are planning a "peaceful demonstration" on November 28 to demand Kabila's resignation in the next month.
On Thursday, the European Union, the United States, Switzerland and Canada expressed "concern" over the state of freedom of expression and assembly in the country.
Its two wars in the late 1990s and early 2000s dragged in at least six African armies and left more than three million dead. The east of the country remains a battleground for rival ethnic militias.
Kabila took office after his father Laurent was assassinated in 2001 at the height of the Second Congo War.
He was confirmed as leader in 2006 during the first free elections since independence, and re-elected for a second term in 2011 in a vote marred by accusations of fraud.