Locals, mistakenly believing that the animals can spread yellow fever to humans, are blamed for the surge in killings.
Just this year, 238 monkeys have been found dead in Rio state, compared to 602 in all of 2017, said the city sanitation service, launching a campaign against the killings.
Of those, 69 percent showed signs of human aggression, mostly being beaten to death and some poisoned. Last year, the proportion found killed by humans was 40 percent.
The rest died of natural causes.
Yellow fever numbers have spiraled in parts of Brazil, causing 25 deaths in Rio state since the start of the year. The government has launched a mass vaccination program but does not have enough vaccine to give everyone the full, lifetime dose.
The monkeys' bodies are collected at an autopsy lab at the Rio Veterinary Center, where coordinator Fabiana Lucena said panicking residents were making a big mistake by attacking the animals.
"People should understand that it's the mosquito transmitting the yellow fever virus. The monkey is a victim and if there are no more monkeys in the countryside, then mosquitoes will come to attack people," she told AFP.
"Monkeys serve as sentinels they show us where the virus has gone," she said.
"To have a more effective vaccination campaign, we have to identify the zones where monkeys are dying from yellow fever. When people kill them, the virus is harder to trace."
A dozen small dead monkeys lay on a table at the lab in preparation for examination.
"Here, you see multiple fractures to the jaws, cervical area, as well as numerous skull traumas," she said, showing a primate's head.
Some of the victims are found right in Rio city, where monkeys are commonly seen in forested areas. The mayor's office has set up a hotline for reporting monkey corpses.
"At the time of the first human deaths from yellow fever in mid-January, we'd sometimes get 20 monkeys found dead in a day, with 18 of them showing signs of attack," Lucena said.
Samples will sometimes be sent to the Osvaldo Cruz research center to be tested for yellow fever and other diseases.
Similar attacks on monkeys have been registered in Sao Paulo and Minas Gerais states, which have seen the worst impact of yellow fever this year.
The latest toll from the Brazilian health ministry is 353 people contracting yellow fever in January and 98 dying between early July and February 6.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)