"Indiscriminate use of force" was used by the police in the run-up to the Olympic Games in August, according to one of the organisations.
In a report handed to the IOC, Terre des Hommes details a 103% increase in police killings compared to 2015.
The IOC is considering recommendations made in the report.
The Rio Games saw 85,000 police staff employed around the city - double the number used at London 2012 - and it led to 90% of tourists rating security as "good" or "excellent".
However, the report - Breaking Records - found evidence of a process of "cleaning" the streets of homeless children, as well as numerous effects resulting from the eviction of 22,000 families between 2009 and 2015 to clear space for the Games.
"Our research reveals human rights violations of youth and children in Rio, ranging from police killings, harsh police repression of protests and an alarming increase of police violence against adolescents in street situation," said Andrea Florence, author of the report.
Renata Neder of Amnesty International Brazil said: "The Olympics were a missed opportunity for public security in Rio de Janeiro.
"We documented a number of violations by security forces, especially a significant increase in the number of people killed by the police and a violent repression of protests."
Specific findings in the report include:
Terre des Hommes called on the IOC to implement measures for future Olympic Games, such as including obligations to comply with international children's rights standards in the host city contract for 2024.
It wants the IOC to communicate with the Rio 2016 local organising committee and Brazilian authorities to ensure they have taken "all appropriate measures related to violations of child rights".
This includes ensuring victims have access to legal advice and that "individual cases are duly investigated, with access to remedy and compensation".
"We call upon the IOC to put in place all measures necessary to avoid repeating the same pattern of violations we have seen in Rio," said Florence.
"Only then will the Games will have a chance to create a better world for generations to come."
The IOC cited a "number of instances" relating to the 2014 Winter Games in Sochi, Russia, where allegations were followed up with the local authorities.
An IOC statement to BBC Sport added: "Where cases are identified - and clearly related to the staging of the Olympic Games - the IOC has a long-standing commitment to follow-up on those issues.
"The IOC can only act on issues that are directly linked to the organisation of the Olympic Games."
The International Olympic Committee should be helping to compensate child victims of police violence at Rio 2016, say children's rights groups.